Methods of producing human foregut endoderm cells expressing pdx1 from human definitive endoderm

ABSTRACT

Disclosed herein are cell cultures comprising dorsal and/or ventral PDX1-positive foregut endoderm cells and methods of producing the same. Also disclosed herein are cell populations comprising substantially purified dorsal and/or ventral PDX1-positive foregut endoderm cells as well as methods for enriching, isolating and purifying dorsal and/or ventral PDX1-positive foregut endoderm cells from other cell types. Methods of identifying differentiation factors capable of promoting the differentiation of dorsal and/or ventral PDX1-positive foregut endoderm cells, are also disclosed.

RELATED APPLICATIONS

This is a continuation of U.S. patent application Ser. No. 16/200,493, filed on Nov. 26, 2018, which is a continuation of U.S. patent application Ser. No. 15/290,850, filed Oct. 11, 2016, abandoned, which is a continuation of U.S. patent application No. Ser. 13/962,978, filed Aug. 9, 2013, issued as U.S. Pat. No. 9,499,795, which is a divisional of U.S. patent application Ser. No. 12/729,084, filed Mar. 22, 2010, abandoned, which is a continuation of U.S. patent application Ser. No. 11/588,693, filed Oct. 27, 2006, abandoned, which claims the benefit of U.S. Provisional Patent Application No. 60/730,917, filed Oct. 27, 2005. The prior applications are all incorporated herein by reference in their entirety.

FIELD OF THE INVENTION

The present invention relates to the fields of medicine and cell biology. In particular, the present invention relates to compositions comprising mammalian foregut endoderm cells and compositions comprising dorsal and/or ventral PDX1-positive foregut endoderm cells and methods of making, isolating and using such cells.

BACKGROUND

Human pluripotent stem cells, such as embryonic stem (ES) cells and embryonic germ (EG) cells, were first isolated in culture without fibroblast feeders in 1994 (Bongso et al., 1994) and with fibroblast feeders (Hogan, 1997). Later, Thomson, Reubinoff and Shamblott established continuous cultures of human ES and EG cells using mitotically inactivated mouse feeder layers (Reubinoff et al., 2000; Shamblott et al., 1998; Thomson et al., 1998).

Human ES and EG cells (hESCs) offer unique opportunities for investigating early stages of human development as well as for therapeutic intervention in several disease states, such as diabetes mellitus and Parkinson's disease. For example, the use of insulin-producing β-cells derived from hESCs would offer a vast improvement over current cell therapy procedures that utilize cells from donor pancreases for the treatment of diabetes. However, presently it is not known how to generate an insulin-producing β-cell from hESCs. As such, current cell therapy treatments for diabetes mellitus, which utilize islet cells from donor pancreases, are limited by the scarcity of high quality islet cells needed for transplant. Cell therapy for a single Type I diabetic patient requires a transplant of approximately 8×10⁸ pancreatic islet cells. (Shapiro et al., 2000; Shapiro et al., 2001a; Shapiro et al., 2001b). As such, at least two healthy donor organs are required to obtain sufficient islet cells for a successful transplant. Human embryonic stem cells offer a source of starting material from which to develop substantial quantities of high quality differentiated cells for human cell therapies.

Two properties that make hESCs uniquely suited to cell therapy applications are pluripotence and the ability to maintain these cells in culture for prolonged periods. Pluripotency is defined by the ability of hESCs to differentiate to derivatives of all 3 primary germ layers (endoderm, mesoderm, ectoderm) which, in turn, form all somatic cell types of the mature organism in addition to extraembryonic tissues (e.g. placenta) and germ cells. Although pluripotency imparts extraordinary utility upon hESCs, this property also poses unique challenges for the study and manipulation of these cells and their derivatives. Owing to the large variety of cell types that may arise in differentiating hESC cultures, the vast majority of cell types are produced at very low efficiencies. Additionally, success in evaluating production of any given cell type depends critically on defining appropriate markers. Achieving efficient, directed differentiation is of great importance for therapeutic application of hESCs.

In order to use hESCs as a starting material to generate cells that are useful in cell therapy applications, it would be advantageous to overcome the foregoing problems. For example, in order to achieve the level of cellular material required for islet cell transplantation therapy, it would be advantageous to efficiently direct hESCs toward the pancreatic islet/β-cell lineage at the very earliest stages of differentiation.

In addition to efficient direction of the differentiation process, it would also be beneficial to isolate and characterize intermediate cell types along the differentiation pathway towards the pancreatic islet/β-cell lineage and to use such cells as appropriate lineage precursors for further steps in the differentiation.

SUMMARY OF THE INVENTION

Embodiments of the present invention relate to cell cultures of PDX1-negative foregut endoderm cells (foregut endoderm cells). In some embodiments, the foregut endoderm expresses the HNF1b and FOXA1 markers but does not substantially express PDX1. Other embodiments of the present invention relate to cell cultures of PDX1-positive, dorsally-biased, foregut endoderm cells (dorsal PDX1-positive foregut endoderm cells). In some embodiments, the PDX1-positive, dorsally-biased, foregut endoderm cells express one or more markers selected from Table 3 and/or one or more markers selected from Table 4. Additional embodiments, relate to cell cultures of PDX1-positive, ventrally-biased, foregut endoderm cells (ventral PDX1-positive foregut endoderm cells). In some embodiments, the PDX1-positive, ventrally-biased, foregut endoderm cells express one or more markers selected from Table 3 but do not substantially express a marker selected from Table 4 as compared to the expression of the same marker in PDX1-positive, dorsally-biased, foregut endoderm cells.

Additional embodiments of the present invention relate to enriched, isolated and/or purified cell populations comprising PDX1-negative foregut endoderm cells. Other embodiments relate to PDX1-positive, dorsally-biased, foregut endoderm cells. Still other embodiments relate to enriched, isolated and/or purified cell populations comprising PDX1-positive, ventrally-biased, foregut endoderm cells.

Aspects of the present invention also relate to methods or processes for the production of cell cultures of PDX1-negative foregut endoderm cells from definitive endoderm cells. Such processes include reducing or eliminating TGFβ superfamily growth factor signaling in a cell culture or cell population of definitive endoderm cells. In some embodiments, reducing or eliminating TGFβ superfamily growth factor signaling is mediated by diluting or removing an exogenously added TGFβ superfamily growth factor, such as activin A, from the cell culture or cell population of definitive endoderm. In some embodiments, differentiation of definitive endoderm cells to foregut endoderm cells is enhanced by providing the definitive endoderm cell culture or cell population with an FGF-family growth factor and/or a hedgehog pathway inhibitor. In some embodiments, the definitive endoderm cells are derived from stem cells. Preferably, the stem cells are embryonic stem cells. Even more preferably, the stem cells are human embryonic stem cells (hESCs). In some embodiments, the PDX1-negative foregut endoderm cells are differentiated to PDX1-positive endoderm cells (pancreatic endoderm cells) by the addition of a retinoid, such as retinoic acid. Other aspects relate to methods or processes for the production of cell cultures of PDX1-positive, dorsally-biased, foregut endoderm cells. Such processes include providing definitive endoderm cells with retinoic acid. In some embodiments, the definitive endoderm cells are derived from stem cells. Preferably, the stem cells are embryonic stem cells. Even more preferably, the stem cells are human embryonic stem cells (hESCs). Further aspects of the present invention relate to methods or processes for the production of cell cultures of PDX1-positive, ventrally-biased, foregut endoderm cells. Such processes include providing definitive endoderm cells with an FGF-family growth factor. In some embodiments, the definitive endoderm cells are derived from stem cells. Preferably, the stem cells are embryonic stem cells. Even more preferably, the stem cells are hESCs.

Additional embodiments of the present invention relate to methods of enriching, isolating and/or purifying PDX1-negative foregut endoderm cells. In such embodiments, PDX1-negative foregut endoderm cells are separated from other cells in the cell population by using an antibody, ligand or other molecule that binds to a molecule that is expressed on the cell surface of PDX1-negative foregut endoderm cells, such as a cell surface molecule. Other embodiments of the present invention relate to methods of enriching, isolating and/or purifying PDX1-positive, dorsally-biased, foregut endoderm cells. In such embodiments, PDX1-positive, dorsally-biased, foregut endoderm cells are separated from other cells in the cell population by using an antibody, ligand or other molecule that binds to a molecule that is expressed on the cell surface of PDX1-positive, dorsally-biased, foregut endoderm cells, such as a cell surface molecule selected from Table 3 or a cell surface molecule selected from Table 4. Still other embodiments of the present invention relate to methods of enriching, isolating and/or purifying PDX1-positive, ventrally-biased, foregut endoderm cells. In such embodiments, PDX1-positive, ventrally-biased, foregut endoderm cells are separated from other cells in the cell population by using an antibody, ligand or other molecule that binds to a molecule that is expressed on the cell surface of PDX1-positive, ventrally-biased, foregut endoderm cells, such as a cell surface molecule selected from Table 3.

Embodiments of the present invention relate to additional methods of enriching, isolating and/or purifying PDX1-negative foregut endoderm cells. In such embodiments, pluripotent or multipotent cells that are precursors to PDX1-negative foregut endoderm cells are engineered to contain a fluorescent reporter gene under control of a promoter that endogenously controls the expression of a marker gene such as HNF1b or FOXA 1. The fluorescently-tagged PDX1-negative foregut endoderm cells are then separated from other cells in the cell population by fluorescence activated cell sorting (FACS). Still other embodiments of the present invention relate to additional methods of enriching, isolating and/or purifying PDX1-positive, dorsally-biased, foregut endoderm cells. In such embodiments, pluripotent or multipotent PDX1-negative cells that are precursors to PDX1-positive cells are engineered to contain a fluorescent reporter gene under control of a promoter that endogenously controls the expression of a marker gene selected from Table 3 or Table 4. The fluorescently-tagged PDX1-positive, dorsally-biased, foregut endoderm cells are then separated from other cells in the cell population by fluorescence activated cell sorting (FACS). Yet other embodiments of the present invention relate to additional methods of enriching, isolating and/or purifying PDX1-positive, ventrally-biased, foregut endoderm cells. In such embodiments, pluripotent or multipotent PDX1-negative cells that are precursors to PDX1-positive cells are engineered to contain a fluorescent reporter gene under control of a promoter that endogenously controls the expression of a marker gene selected from Table 3. The fluorescently-tagged PDX1-positive, ventrally-biased, foregut endoderm cells are then separated from other cells in the cell population by FACS.

Further embodiments of the present invention relate to methods of identifying a differentiation factor capable of promoting the differentiation of human PDX1-negative foregut endoderm cells in a cell population comprising human cells. The method includes the steps of obtaining a cell population comprising human PDX1-negative foregut endoderm cells, providing a candidate differentiation factor to the cell population, determining expression of a marker, such as HNF1b, FOXA1 or PDX1, in the cell population at a first time point and determining expression of the same marker in the cell population at a second time point. In such embodiments, the second time point is subsequent to the first time point and the second time point is subsequent to providing the cell population with the candidate differentiation factor. If expression of the marker in the cell population at the second time point is increased or decreased as compared to the expression of the marker in the cell population at the first time point, then the candidate differentiation factor is capable of promoting the differentiation of the human PDX1-negative foregut endoderm cells. Still further embodiments of the present invention relate to methods of identifying a differentiation factor capable of promoting the differentiation of human PDX1-positive, dorsally-biased, foregut endoderm cells in a cell population comprising human cells. The method includes the steps of obtaining a cell population comprising human PDX1-positive, dorsally-biased, foregut endoderm cells, providing a candidate differentiation factor to the cell population, determining expression of a marker, such as a marker selected from Table 3 or a marker selected from Table 4, in the cell population at a first time point and determining expression of the same marker in the cell population at a second time point. In such embodiments, the second time point is subsequent to the first time point and the second time point is subsequent to providing the cell population with the candidate differentiation factor. If expression of the marker in the cell population at the second time point is increased or decreased as compared to the expression of the marker in the cell population at the first time point, then the candidate differentiation factor is capable of promoting the differentiation of the human PDX1-positive, dorsally-biased, foregut endoderm cells. Yet further embodiments of the present invention relate to methods of identifying a differentiation factor capable of promoting the differentiation of human PDX1-positive, ventrally-biased, foregut endoderm cells in a cell population comprising human cells. The method includes the steps of obtaining a cell population comprising human PDX1-positive, ventrally-biased, foregut endoderm cells, providing a candidate differentiation factor to the cell population, determining expression of a marker, such as a marker selected from Table 3, in the cell population at a first time point and determining expression of the same marker in the cell population at a second time point. In such embodiments, the second time point is subsequent to the first time point and the second time point is subsequent to providing the cell population with the candidate differentiation factor. If expression of the marker in the cell population at the second time point is increased or decreased as compared to the expression of the marker in the cell population at the first time point, then the candidate differentiation factor is capable of promoting the differentiation of the human PDX1-positive, ventrally-biased, foregut endoderm cells.

In certain jurisdictions, there may not be any generally accepted definition of the term “comprising.” As used herein, the term “comprising” is intended to represent “open” language which permits the inclusion of any additional elements. With this in mind, additional embodiments of the present inventions are described with reference to the numbered paragraphs below:

1. A cell culture comprising human cells wherein at least about 26% of said human cells are pancreatic-duodenal homoebox factor-1 (PDX1) positive, dorsally-biased, foregut endoderm cells that express at least one marker selected from Table 3, said PDX1-positive, dorsally-biased, foregut endoderm cells being multipotent cells that can differentiate into cells of the dorsal pancreatic bud.

2. The cell culture of paragraph 1, wherein said marker selected from Table 3 is a marker expressed on the cell surface.

3. The cell culture of paragraph 2, wherein said marker expressed on the cell surface is selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2 and SLC27A2.

4. The cell culture of paragraph 1, wherein said PDX1-positive, dorsally-biased, foregut endoderm cells express at least one marker selected from Table 4.

5. The cell culture of paragraph 4, wherein said marker selected from Table 4 is a marker expressed on the cell surface.

6. The cell culture of paragraph 5, wherein said marker expressed on the cell surface is selected from the group consisting of ADORA2A, CD47, EPB41L1, MAG, SFRPS, SLC16A10, SLC16A2, SLC1A3, SLC30A4, SLICK, SLITRK4 and XPR1.

7. The cell culture of paragraph 1, wherein at least about 30% of said human cells are PDX1-positive, dorsally-biased, foregut endoderm cells.

8. The cell culture of paragraph 1, wherein at least about 40% of said human cells are PDX1-positive, dorsally-biased, foregut endoderm cells.

9. The cell culture of paragraph 1, wherein at least about 50% of said human cells are PDX1-positive, dorsally-biased, foregut endoderm cells.

10. The cell culture of paragraph 1, wherein at least about 60% of said human cells are PDX1-positive, dorsally-biased, foregut endoderm cells.

11. The cell culture of paragraph 1, wherein at least about 75% of said human cells are PDX1-positive, dorsally-biased, foregut endoderm cells.

12. The cell culture of paragraph 1, wherein human feeder cells are present in said culture, and wherein at least about 2% of human cells other than said human feeder cells are PDX1-positive, dorsally biased, foregut endoderm cells.

13. The cell culture of paragraph 1, wherein the expression of PDX1 is greater than the expression of a marker selected from the group consisting of alpha-fetoprotein (AFP), SOX7, SOX1, ZIC1 and NFM in said PDX1-positive, dorsally biased, foregut endoderm cells.

14. The cell culture of paragraph 1, wherein said cell culture is substantially free of cells selected from the group consisting of visceral endodermal cells, parietal endodermal cells and neural cells.

15. The cell culture of paragraph 1 further comprising a retinoid.

16. The cell culture of paragraph 15, wherein said retinoid is retinoic acid (RA).

17. The cell culture of paragraph 16 further comprising B27.

18. A cell culture comprising human cells wherein at least about 2% of said human cells are pancreatic-duodenal homoebox factor-1 (PDX1) positive, ventrally-biased, foregut endoderm cells that express at least one marker selected from Table 3, said PDX1-positive, ventrally-biased, foregut endoderm cells being multipotent cells that can differentiate into cells of the ventral pancreatic bud.

19. The cell culture of paragraph 18, wherein said marker selected from Table 3 is a marker expressed on the cell surface.

20. The cell culture of paragraph 19, wherein said marker expressed on the cell surface is selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2 and SLC27A2.

21. The cell culture of paragraph 18, wherein said PDX1-positive, ventrally-biased, foregut endoderm cells do not substantially express one or more markers selected from Table 4.

22. The cell culture of paragraph 18, wherein at least about 5% of said human cells are PDX1-positive, ventrally-biased, foregut endoderm cells.

23. The cell culture of paragraph 18, wherein at least about 10% of said human cells are PDX1-positive, ventrally-biased, foregut endoderm cells.

24. The cell culture of paragraph 18, wherein at least about 25% of said human cells are PDX1-positive, ventrally-biased, foregut endoderm cells.

25. The cell culture of paragraph 18, wherein at least about 50% of said human cells are PDX1-positive, ventrally-biased, foregut endoderm cells.

26. The cell culture of paragraph 18, wherein at least about 75% of said human cells are PDX1-positive, ventrally-biased, foregut endoderm cells.

27. The cell culture of paragraph 18, wherein human feeder cells are present in said culture, and wherein at least about 2% of human cells other than said human feeder cells are PDX1-positive, ventrally-biased, foregut endoderm cells.

28. The cell culture of paragraph 18, wherein the expression of PDX1 is greater than the expression of a marker selected from the group consisting of alpha-fetoprotein (AFP), SOX7, SOX1, ZIC1 and NFM in said PDX1-positive, ventrally-biased, foregut endoderm cells.

29. The cell culture of paragraph 18, wherein said cell culture is substantially free of cells selected from the group consisting of visceral endodermal cells, parietal endodermal cells and neural cells.

30. The cell culture of paragraph 18 further comprising a retinoid.

31. The cell culture of paragraph 30, wherein said retinoid is retinoic acid (RA).

32. The cell culture of paragraph 31 further comprising B27.

33. A cell population comprising cells wherein at least about 90% of said cells are human PDX1-positive, dorsally-biased, foregut endoderm cells that express at least one marker selected from Table 3, said PDX1-positive, dorsally-biased, foregut endoderm cells being multipotent cells that can differentiate into cells of the dorsal pancreatic bud.

34. The cell population of paragraph 33, wherein said marker selected from Table 3 is a marker expressed on the cell surface.

35. The cell population of paragraph 34, wherein said marker expressed on the cell surface is selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2 and SLC27A2.

36. The cell population of paragraph 33, wherein said PDX1-positive, dorsally-biased, foregut endoderm cells express at least one marker selected from Table 4.

37. The cell population of paragraph 36, wherein said marker selected from Table 4 is a marker expressed on the cell surface.

38. The cell population of paragraph 37, wherein said marker expressed on the cell surface is selected from the group consisting of ADORA2A, CD47, EPB41L1, MAG, SFRPS, SLC16A10, SLC16A2, SLC1A3, SLC30A4, SLICK, SLITRK4 and XPR1.

39. The cell population of paragraph 33, wherein at least about 95% of said cells are PDX1-positive, dorsally-biased, foregut endoderm cells.

40. The cell population of paragraph 33, wherein at least about 98% of said cells are PDX1-positive, dorsally-biased, foregut endoderm cells.

41. The cell population of paragraph 33, wherein the expression of PDX1 is greater than the expression of a marker selected from the group consisting of AFP, SOX7, SOX1, ZIC1 and NFM in said PDX1-positive, dorsally-biased, foregut endoderm cells.

42. A cell population comprising cells wherein at least about 90% of said cells are human PDX1-positive, ventrally-biased, foregut endoderm cells that express at least one marker selected from Table 3, said PDX1-positive, ventrally-biased, foregut endoderm cells being multipotent cells that can differentiate into cells of the ventral pancreatic bud.

43. The cell population of paragraph 42, wherein said marker selected from Table 3 is a marker expressed on the cell surface.

44. The cell population of paragraph 43, wherein said marker expressed on the cell surface is selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2 and SLC27A2.

45. The cell population of paragraph 42, wherein said PDX1-positive, ventrally-biased, foregut endoderm cells do not substantially express one or more markers selected from Table 4.

46. The cell population of paragraph 42, wherein at least about 95% of said cells are PDX1-positive, ventrally-biased, foregut endoderm cells.

47. The cell population of paragraph 42, wherein at least about 98% of said cells are PDX1-positive, ventrally-biased, foregut endoderm cells.

48. The cell population of paragraph 42, wherein the expression of PDX1 is greater than the expression of a marker selected from the group consisting of AFP, SOX7, SOX1, ZIC1 and NFM in said PDX1-positive, ventrally-biased, foregut endoderm cells.

49. A method of producing PDX1-positive, dorsally-biased, foregut endoderm cells, said method comprising the steps of obtaining a cell population comprising PDX1-negative definitive endoderm cells and providing said cell population with a retinoid in an amount sufficient to promote differentiation of at least 26% of said PDX1-negative definitive endoderm cell population to PDX1-positive, dorsally-biased, foregut endoderm cells that express at least one marker selected from Table 3, wherein said PDX1-positive, dorsally-biased, foregut endoderm cells are multipotent cells that can differentiate into cells of the dorsal pancreatic bud.

50. The method of paragraph 49, wherein said PDX1-positive, dorsally-biased, foregut endoderm cells also express at least one marker selected from Table 4.

51. The method of paragraph 50 further comprising the step of allowing sufficient time for PDX1-positive, dorsally-biased, foregut endoderm cells to form, wherein said sufficient time for PDX1-positive, dorsally-biased, foregut endoderm cells to form has been determined by detecting the presence of a marker from Table 4 in dorsally-biased foregut endoderm cells in said cell population.

52. The method of paragraph 50, wherein the expression of said marker selected from Table 3 or Table 4 is determined by quantitative polymerase chain reaction (Q-PCR).

53. The method of paragraph 50, wherein the expression of said marker selected from Table 3 or Table 4 is determined by immunocytochemistry.

54. The method of paragraph 49, wherein the expression of PDX1 is greater than the expression of a marker selected from the group consisting of alpha-fetoprotein (AFP), SOX7, SOX1, ZIC1 and NFM in said PDX1-positive, dorsally-biased, foregut endoderm cells.

55. The method of paragraph 49, wherein said retinoid is RA.

56. The method of paragraph 55, wherein RA is provided in a concentration ranging from about 0.5 μM to about 50 μM.

57. The method of paragraph 56, wherein RA is provided in a concentration ranging from about 1 μM to about 20 μM.

58. The method of paragraph 57, wherein RA is provided in a concentration of about 2 μM.

59. The method of paragraph 55, wherein RA is provided when said culture is about 5-days-old.

60. The method of paragraph 49 further comprising providing B27 to said culture.

61. The method of paragraph 60, wherein said B27 is provided in a concentration ranging from about 0.1% to about 20% of the total medium.

62. The method of paragraph 61, wherein B27 is provided in a concentration ranging from about 0.5% to about 2% of the total medium.

63. The method of paragraph 62, wherein B27 is provided in a concentration of about 0.5% of the total medium.

64. The method of paragraph 60, wherein B27 is provided at approximately the same time as said retinoid.

65. The method of paragraph 49 further comprising providing activin A to said culture.

66. The method of paragraph 65, wherein activin A is provided in a concentration ranging from about 10 ng/ml to about 200 ng/ml.

67. The method of paragraph 66, wherein activin A is provided in a concentration ranging from about 20 ng/ml to about 100 ng/ml.

68. The method of paragraph 67, wherein activin A is provided in a concentration of about 25 ng/ml.

69. The method of paragraph 49, wherein said PDX1-positive, dorsally-biased, foregut endoderm cells are grown in CMRL medium.

70. The method of paragraph 69, wherein said CMRL medium comprises RA at about 2 μM, activin A at about 25 ng/ml and B27 at about 0.5% of the total medium.

71. The method of paragraph 49, wherein said step of obtaining a cell population comprising PDX1-negative definitive endoderm cells comprises obtaining a cell population comprising pluripotent human cells, providing said cell population with at least one growth factor of the TGFβ superfamily in an amount sufficient to promote differentiation of said pluripotent cells to definitive endoderm cells and allowing sufficient time for definitive endoderm cells to form, wherein said sufficient time for definitive endoderm cells to form has been determined by detecting the presence of definitive endoderm cells in said cell population.

72. A PDX1-positive, dorsally-biased, foregut endoderm cell produced by the method of paragraph 49.

73. A method of producing PDX1-positive, ventrally-biased, foregut endoderm cells, said method comprising the steps of obtaining a cell population comprising PDX1-negative definitive endoderm cells and providing said cell population with an FGF-family growth factor in an amount sufficient to promote differentiation of at least a portion of said PDX1-negative definitive endoderm cell population to PDX1-positive, ventrally-biased, foregut endoderm cells that express at least one marker selected from Table 3, wherein said PDX1-positive, ventrally-biased, foregut endoderm cells are multipotent cells that can differentiate into cells of the ventral pancreatic bud.

74. The method of paragraph 73, wherein said cell population is differentiated in the absence of RA.

75. The method of paragraph 73, wherein said PDX1-positive, ventrally-biased, foregut endoderm cells do not express one or more markers selected from Table 4.

76. The method of paragraph 75 further comprising the step of allowing sufficient time for PDX1-positive, ventrally-biased, foregut endoderm cells to form, wherein said sufficient time for PDX1-positive, ventrally-biased, foregut endoderm cells to form has been determined by detecting the presence of a marker from Table 3 in ventrally-biased foregut endoderm cells in said cell population.

77. The method of paragraph 76, wherein the expression of said marker selected from Table 3 is determined by quantitative polymerase chain reaction (Q-PCR).

78. The method of paragraph 76, wherein the expression of said marker selected from Table 3 is determined by immunocytochemistry.

79. The method of paragraph 73, wherein the expression of PDX1 is greater than the expression of a marker selected from the group consisting of alpha-fetoprotein (AFP), SOX7, SOX1, ZIC1 and NFM in said PDX1-positive, ventrally-biased, foregut endoderm cells.

80. The method of paragraph 73, wherein said FGF-family growth factor is FGF-10, said FGF-10 being provided in a concentration ranging from about 5 ng/ml to about 500 ng/ml.

81. The method of paragraph 80, wherein FGF-10 is provided in a concentration ranging from about 10 ng/ml to about 100 ng/ml.

82. The method of paragraph 81, wherein FGF-10 is provided in a concentration of about 50 ng/ml.

83. The method of paragraph 73, wherein said FGF-family growth factor is provided when said culture is about 3-days-old.

84. The method of paragraph 73 further comprising providing B27 to said culture.

85. The method of paragraph 84, wherein said B27 is provided in a concentration ranging from about 0.1% to about 20% of the total medium.

86. The method of paragraph 85, wherein B27 is provided in a concentration ranging from about 0.5% to about 2% of the total medium.

87. The method of paragraph 86, wherein B27 is provided in a concentration of about 0.5% of the total medium.

88. The method of paragraph 84, wherein B27 is provided at approximately the same time as said FGF-family growth factor.

89. The method of paragraph 73 further comprising providing a hedgehog inhibitor to said culture

90. The method of paragraph 89, wherein said hedgehog inhibitor is KAAD-cyclopamine, said KAAD-cyclopamine being provided in a concentration of about 0.1 μM to about 50 μM.

91. The method of paragraph 90, wherein KAAD-cyclopamine is provided in a concentration ranging from about 0.5 μM to about 10 μM.

92. The method of paragraph 91, wherein KAAD-cyclopamine is provided in a concentration of about 0.5 μM.

93. The method of paragraph 73, wherein said PDX1-positive, ventrally-biased, foregut endoderm cells are grown in CMRL medium.

94. The method of paragraph 93, wherein said CMRL medium comprises FGF-10 at about 50 ng/ml, KAAD-cyclopamine at about 0.5 μM, and B27 at about 0.5% of the total medium.

95. The method of paragraph 94, wherein said CMRL medium lacks RA.

96. The method of paragraph 73, wherein said step of obtaining a cell population comprising PDX1-negative definitive endoderm cells comprises obtaining a cell population comprising pluripotent human cells, providing said cell population with at least one growth factor of the TGFβ superfamily in an amount sufficient to promote differentiation of said pluripotent cells to definitive endoderm cells and allowing sufficient time for definitive endoderm cells to form, wherein said sufficient time for definitive endoderm cells to form has been determined by detecting the presence of definitive endoderm cells in said cell population.

97. A PDX1-positive, ventrally-biased, foregut endoderm cell produced by the method of paragraph 73.

98. A method of producing a cell population enriched in PDX1-positive, dorsally-biased, foregut endoderm cells, said method comprising the steps of differentiating cells in a population of PDX1-negative definitive endoderm cells so as to produce PDX1-positive, dorsally-biased, foregut endoderm cells, said PDX1-positive, dorsally-biased, foregut endoderm cells being multipotent cells that can differentiate into cells of the dorsal pancreatic bud, providing to said cell population a reagent which binds to a marker expressed in said PDX1-positive, dorsally-biased, foregut endoderm cells but which is not substantially expressed in other cell types present in said cell population and separating said PDX1-positive, dorsally-biased, foregut endoderm cells bound to said reagent from said other cell types present in said cell population, thereby producing a cell population enriched in PDX1-positive, dorsally-biased, foregut endoderm cells.

99. The method for paragraph 98, wherein said marker is selected from the group consisting of ADORA2A, CD47, EPB41L1, MAG, SFRP5, SLC16A10, SLC16A2, SLC1A3, SLC30A4, SLICK, SLITRK4 and XPR1.

100. The method for paragraph 98, wherein said marker is selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2 and SLC27A2.

101. The method of paragraph 98, wherein the differentiating step further comprises obtaining a cell population comprising PDX1-negative definitive endoderm cells, providing said cell population with a retinoid in an amount sufficient to promote differentiation of said PDX1-negative definitive endoderm cells to PDX1-positive, dorsally-biased, foregut endoderm cells, said PDX1-positive, dorsally-biased, foregut endoderm cells being multipotent cells that can differentiate into cells of the dorsal pancreatic bud, and allowing sufficient time for PDX1-positive, dorsally-biased, foregut endoderm cells to form, wherein said sufficient time for PDX1-positive, dorsally-biased, foregut endoderm cells to form has been determined by detecting the presence of PDX1-positive, dorsally-biased, foregut endoderm cells in said cell population.

102. The method of paragraph 101, wherein the providing step further comprises providing B27.

103. The method of paragraph 101, wherein detecting comprises detecting the expression of at least one marker selected from Table 4.

104. The method of paragraph 98, wherein at least about 95% of said cells are PDX1-positive, dorsally-biased, foregut endoderm cells.

105. The method of paragraph 98, wherein at least about 98% of said cells are PDX1-positive, dorsally-biased, foregut endoderm cells.

106. The method of paragraph 98, wherein said reagent is an antibody

107. The method of paragraph 106, wherein said antibody has affinity for a cell surface polypeptide selected from the group consisting of ADORA2A, CD47, EPB41L1, MAG, SFRPS, SLC16A10, SLC16A2, SLC1A3, SLC30A4, SLICK, SLITRK4, XPR1, CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2 and SLC27A2.

108. An enriched population of PDX1-positive, dorsally-biased, foregut endoderm cells produced by the method of paragraph 98.

109. A method of producing a cell population enriched in PDX1-positive, ventrally-biased, foregut endoderm cells, said method comprising the steps of differentiating cells in a population of PDX1-negative definitive endoderm cells so as to produce PDX1-positive, ventrally-biased, foregut endoderm cells, said PDX1-positive, ventrally-biased, foregut endoderm cells being multipotent cells that can differentiate into cells of the ventral pancreatic bud, providing to said cell population a reagent which binds to a marker expressed in said PDX1-positive, ventrally-biased, foregut endoderm cells but which is not substantially expressed in other cell types present in said cell population and separating said PDX1-positive, ventrally-biased, foregut endoderm cells bound to said reagent from said other cell types present in said cell population, thereby producing a cell population enriched in PDX1-positive, ventrally-biased, foregut endoderm cells.

110. The method for paragraph 109, wherein said marker is selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2 and SLC27A2.

111. The method of paragraph 109, wherein the differentiating step further comprises obtaining a cell population comprising PDX1-negative definitive endoderm cells, providing said cell population with an FGF-family growth factor in an amount sufficient to promote differentiation of said PDX1-negative definitive endoderm cells to PDX1-positive, ventrally-biased, foregut endoderm cells, said PDX1-positive, ventrally-biased, foregut endoderm cells being multipotent cells that can differentiate into cells of the ventral pancreatic bud, and allowing sufficient time for PDX1-positive, ventrally-biased, foregut endoderm cells to form, wherein said sufficient time for PDX1-positive, ventrally-biased, foregut endoderm cells to form has been determined by detecting the presence of PDX1-positive, ventrally-biased, foregut endoderm cells in said cell population.

112. The method of paragraph 111, wherein the providing step further comprises providing B27.

113. The method of paragraph 111, wherein detecting comprises detecting the expression of at least one marker selected from Table 3.

114. The method of paragraph 109, wherein at least about 95% of said cells are PDX1-positive, ventrally-biased, foregut endoderm cells.

115. The method of paragraph 109, wherein at least about 98% of said cells are PDX I-positive, ventrally-biased, foregut endoderm cells.

116. The method of paragraph 109, wherein said reagent is an antibody

117. The method of paragraph 116, wherein said antibody has affinity for a cell surface polypeptide selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2 and SLC27A2.

118. An enriched population of PDX I-positive, ventrally-biased, foregut endoderm cells produced by the method of paragraph 109.

119. A method of producing a cell population enriched in PDX1-positive, dorsally-biased, foregut endoderm cells, said method comprising the steps of obtaining a population of pluripotent cells, wherein at least one cell of said pluripotent cell population comprises at least one copy of a nucleic acid under the control of the a promoter of any one of the marker genes selected from Table 4, said nucleic acid comprising a sequence encoding a fluorescent protein or a biologically active fragment thereof, differentiating said pluripotent cells so as to produce PDX I-positive, dorsally-biased foregut endoderm cells, said PDX1-positive, dorsally-biased, foregut endoderm cells being multipotent cells that can differentiate into cells of the dorsal pancreatic bud, and separating said PDX I-positive, dorsally-biased, foregut endoderm cells from other cell types present in the cell population.

120. The method of paragraph 119, wherein said enriched cell population comprises at least about 95% PDX I-positive, dorsally-biased, foregut endoderm cells.

121. The method of paragraph 119, wherein said enriched cell population comprises at least about 98% PDX1-positive, dorsally-biased, foregut endoderm cells.

122. The method of paragraph 119, wherein the differentiating step further comprises, providing said pluripotent cell population with at least one growth factor of the TGFβ superfamily in an amount sufficient to promote differentiation of said pluripotent cells to PDX I-negative definitive endoderm cells, and providing said PDX I-negative definitive endoderm cells with a retinoid in an amount sufficient to promote differentiation of said PDX1-negative definitive endoderm cells to PDX1-positive, dorsally-biased, foregut endoderm cells.

123. The method of paragraph 122, wherein said retinoid is RA.

124. The method of paragraph 123, wherein the providing step further comprises providing B27.

125. The method of paragraph 119, wherein said fluorescent protein is green fluorescent protein (GFP).

126. The method of paragraph 119, wherein said PDX1-positive, dorsally-biased, foregut endoderm cells are separated from other cell types present in the cell population by fluorescence activated cell sorting (FACS).

127. An enriched population of PDX1-positive, dorsally-biased, foregut endoderm cells produced by the method of paragraph 119.

128. A method of producing a cell population enriched in PDX1-positive, ventrally-biased, foregut endoderm cells, said method comprising the steps of obtaining a population of pluripotent cells, wherein at least one cell of said pluripotent cell population comprises at least one copy of a nucleic acid under the control of the a promoter of any one of the marker genes selected from Table 3, said nucleic acid comprising a sequence encoding a fluorescent protein or a biologically active fragment thereof, differentiating said pluripotent cells so as to produce PDX1-positive, ventrally-biased foregut endoderm cells, said PDX1-positive, ventrally-biased, foregut endoderm cells being multipotent cells that can differentiate into cells of the ventral pancreatic bud and separating said PDX1-positive, ventrally-biased, foregut endoderm cells from non-ventrally-biased foregut endoderm cells.

129. The method of paragraph 128, wherein said enriched cell population comprises at least about 95% PDX1-positive, ventrally-biased, foregut endoderm cells.

130. The method of paragraph 128, wherein said enriched cell population comprises at least about 98% PDX1-positive, ventrally-biased, foregut endoderm cells.

131. The method of paragraph 128, wherein the differentiating step further comprises, providing said pluripotent cell population with at least one growth factor of the TGFβ superfamily in an amount sufficient to promote differentiation of said pluripotent cells to PDX1-negative definitive endoderm cells, and providing said PDX1-negative definitive endoderm cells with an FGF-family growth factor in an amount sufficient to promote differentiation of said PDX1-negative definitive endoderm cells to PDX1-positive, ventrally-biased, foregut endoderm cells.

132. The method of paragraph 128, wherein the providing step further comprises providing B27.

133. The method of paragraph 128, wherein said fluorescent protein is green fluorescent protein (GFP).

134. The method of paragraph 128, wherein said PDX1-positive, dorsally-biased, foregut endoderm cells are separated from other cell types present in the cell population by fluorescence activated cell sorting (FACS).

135. An enriched population of PDX1-positive, dorsally-biased, foregut endoderm cells produced by the method of paragraph 128.

136. A method of identifying a differentiation factor capable of promoting the differentiation of human PDX1-positive, dorsally-biased, foregut endoderm cells in a cell population comprising human cells, said method comprising the steps of obtaining a cell population comprising human PDX1-positive, dorsally-biased, foregut endoderm cells, providing a candidate differentiation factor to said cell population, determining expression of a marker in said cell population at a first time point, determining expression of the same marker in said cell population at a second time point, wherein said second time point is subsequent to said first time point and wherein said second time point is subsequent to providing said cell population with said candidate differentiation factor and determining if expression of the marker in said cell population at said second time point is increased or decreased as compared to the expression of the marker in said cell population at said first time point, wherein an increase or decrease in expression of said marker in said cell population indicates that said candidate differentiation factor is capable of promoting the differentiation of said human PDX1-positive, dorsally-biased, foregut endoderm cells.

137. The method of paragraph 136, wherein said marker is selected from Table 4.

138. The method of paragraph 136, wherein said human PDX1-positive, dorsally-biased, foregut endoderm cells comprise at least about 10% of the human cells in said cell population.

139. The method of paragraph 136, wherein human feeder cells are present in said cell population and wherein at least about 10% of the human cells other than said feeder cells are PDX1-positive, dorsally-biased, foregut endoderm cells.

140. The method of paragraph 136, wherein said human PDX1-positive, dorsally-biased, foregut endoderm cells comprise at least about 90% of the human cells in said cell population.

141. The method of paragraph 136, wherein said human feeder cells are present in said cell population and wherein at least about 90% of the human cells other than said feeder cells are PDX1-positive, dorsally-biased, foregut endoderm cells.

142. The method of paragraph 136, wherein said human PDX1-positive, dorsally-biased, foregut endoderm cells can differentiate into cells of the dorsal pancreatic bud.

143. The method of paragraph 136, wherein said human definitive endoderm cells differentiate into pancreatic precursor cells in response to said candidate differentiation factor.

144. The method of paragraph 136, wherein said first time point is prior to providing said candidate differentiation factor to said cell population.

145. The method of paragraph 136, wherein said first time point is at approximately the same time as providing said candidate differentiation factor to said cell population.

146. The method of paragraph 136, wherein said first time point is subsequent to providing said candidate differentiation factor to said cell population.

147. The method of paragraph 136, wherein expression of said marker is increased.

148. The method of paragraph 136, wherein expression of said marker is decreased.

149. The method of paragraph 136, wherein expression of said marker is determined by quantitative polymerase chain reaction (Q-PCR).

150. The method of paragraph 136, wherein expression of said marker is determined by immunocytochemistry.

151. The method of paragraph 136, wherein said differentiation factor comprises a small molecule.

152. The method of paragraph 136, wherein said differentiation factor comprises a polypeptide.

153. The method of paragraph 136, wherein said differentiation factor comprises a growth factor.

154. A method of identifying a differentiation factor capable of promoting the differentiation of human PDX1-positive, ventrally-biased, foregut endoderm cells in a cell population comprising human cells, said method comprising the steps of obtaining a cell population comprising human PDX1-positive, ventrally-biased, foregut endoderm cells, providing a candidate differentiation factor to said cell population, determining expression of a marker in said cell population at a first time point, determining expression of the same marker in said cell population at a second time point, wherein said second time point is subsequent to said first time point and wherein said second time point is subsequent to providing said cell population with said candidate differentiation factor and determining if expression of the marker in said cell population at said second time point is increased or decreased as compared to the expression of the marker in said cell population at said first time point, wherein an increase or decrease in expression of said marker in said cell population indicates that said candidate differentiation factor is capable of promoting the differentiation of said human PDX1-positive, ventrally-biased, foregut endoderm cells.

155. The method of paragraph 154, wherein said marker is selected from Table 3.

156. The method of paragraph 154, wherein said human PDX1-positive, ventrally-biased, foregut endoderm cells comprise at least about 10% of the human cells in said cell population.

157. The method of paragraph 154, wherein human feeder cells are present in said cell population and wherein at least about 10% of the human cells other than said feeder cells are PDX1-positive, ventrally-biased, foregut endoderm cells.

158. The method of paragraph 154, wherein said human PDX1-positive, ventrally-biased, foregut endoderm cells comprise at least about 90% of the human cells in said cell population.

159. The method of paragraph 154, wherein said human feeder cells are present in said cell population and wherein at least about 90% of the human cells other than said feeder cells are PDX1-positive, ventrally-biased, foregut endoderm cells.

160. The method of paragraph 154, wherein said human PDX1-positive, ventrally-biased, foregut endoderm cells can differentiate into cells of the ventral pancreatic bud.

161. The method of paragraph 154, wherein said human definitive endoderm cells differentiate into pancreatic precursor cells in response to said candidate differentiation factor.

162. The method of paragraph 154, wherein said first time point is prior to providing said candidate differentiation factor to said cell population.

163. The method of paragraph 154, wherein said first time point is at approximately the same time as providing said candidate differentiation factor to said cell population.

164. The method of paragraph 154, wherein said first time point is subsequent to providing said candidate differentiation factor to said cell population.

165. The method of paragraph 154, wherein expression of said marker is increased.

166. The method of paragraph 154, wherein expression of said marker is decreased.

167. The method of paragraph 154, wherein expression of said marker is determined by quantitative polymerase chain reaction (Q-PCR).

168. The method of paragraph 154, wherein expression of said marker is determined by immunocytochemistry.

169. The method of paragraph 154, wherein said differentiation factor comprises a small molecule.

170. The method of paragraph 154, wherein said differentiation factor comprises a polypeptide.

171. The method of paragraph 154, wherein said differentiation factor comprises a growth factor.

It will be appreciated that the methods and compositions described above relate to cells cultured in vitro. However, the above-described in vitro differentiated cell compositions may be used for in vivo applications.

Additional embodiments of the present invention may also be found in U.S. Provisional Patent Application No. 60/532,004, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2003; U.S. Provisional Patent Application No. 60/566,293, entitled PDX1 EXPRESSING ENDODERM, filed Apr. 27, 2004; U.S. Provisional Patent Application No. 60/586,566, entitled CHEMOKINE CELL SURFACE RECEPTOR FOR THE ISOLATION OF DEFINITIVE ENDODERM, filed Jul. 9, 2004; U.S. Provisional Patent Application Number 60/587,942, entitled CHEMOKINE CELL SURFACE RECEPTOR FOR THE ISOLATION OF DEFINITIVE ENDODERM, filed Jul. 14, 2004; U.S. patent application Ser. No. 11/021,618, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2004 and U.S. patent application Ser. No. 11/115,868, entitled PDX1 EXPRESSING ENDODERM, filed Apr. 26, 2005; U.S. patent application Ser. No. 11/165,305, entitled METHODS FOR IDENTIFYING FACTORS FOR DIFFERENTIATING DEFINITIVE ENDODERM, filed Jun. 23, 2005, the disclosures of which are incorporated herein by reference in their entireties.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic of a proposed differentiation pathway for the production of beta-cells from hESCs. The first step in the pathway commits the ES cell to the definitive endoderm lineage and also represents the first step prior to further differentiation events to pancreatic endoderm, endocrine endoderm, or islet/beta-cells. The second step in the pathway shows the conversion of SOX17-positive/PDX1-negative definitive endoderm to PDX1-positive foregut endoderm. Some factors useful for mediating these transitions are italicized. Relevant markers for defining the target cells are underlined.

FIG. 2 is a diagram of the human SOX17 cDNA which displays the positions of conserved motifs and highlights the region used for the immunization procedure by GENOVAC.

FIG. 3 is a relational dendrogram illustrating that SOX17 is most closely related to SOX7 and somewhat less to SOX18. The SOX17 proteins are more closely related among species homologs than to other members of the SOX group F subfamily within the same species.

FIG. 4 is a Western blot probed with the rat anti-SOX17 antibody. This blot demonstrates the specificity of this antibody for human SOX17 protein over-expressed in fibroblasts (lane 1) and a lack of immunoreactivity with EGFP (lane 2) or the most closely related SOX family member, SOX7 (lane 3).

FIGS. 5A-5B are micrographs showing a cluster of SOX17⁺ cells that display a significant number of AFP co-labeled cells (A). This is in striking contrast to other SOX17⁺ clusters (B) where little or no AFP cells are observed.

FIGS. 6A-6C are micrographs showing parietal endoderm and SOX17. Panel A shows immunocytochemistry for human Thrombomodulin (TM) protein located on the cell surface of parietal endoderm cells in randomly differentiated cultures of hES cells. Panel B is the identical field shown in A double-labeled for TM and SOX17. Panel C is the phase contrast image of the same field with DAPI labeled nuclei. Note the complete correlation of DAPI labeled nuclei and SOX17 labeling.

FIGS. 7A-7B are bar charts showing SOX17 gene expression by quantitative PCR (Q-PCR) and anti-SOX17 positive cells by SOX17-specific antibody. Panel A shows that activin A increases SOX17 gene expression while retinoic acid (RA) strongly suppresses SOX17 expression relative to the undifferentiated control media (SR20). Panel B shows the identical pattern as well as a similar magnitude of these changes is reflected in SOX17⁺ cell number, indicating that Q-PCR measurement of SOX17 gene expression is very reflective of changes at the single cell level.

FIGS. 8A-8C. FIG. 8A is a bar chart which shows that a culture of differentiating hESCs in the presence of activin A maintains a low level of AFP gene expression while cells allowed to randomly differentiate in 10% fetal bovine serum (FBS) exhibit a strong upregulation of AFP. The difference in expression levels is approximately 7-fold.

FIGS. 8B-8C are images of two micrographs showing that the suppression of AFP expression by activin A is also evident at the single cell level as indicated by the very rare and small clusters of AFP cells observed in activin A treatment conditions (bottom) relative to 10% FBS alone (top).

FIGS. 9A-9B are comparative images showing the quantitation of the AFP cell number using flow cytometry. This figure demonstrates that the magnitude of change in AFP gene expression (FIG. 8A) in the presence (right panel) and absence (left panel) of activin A exactly corresponds to the number of AFP cells, further supporting the utility of Q-PCR analyses to indicate changes occurring at the individual cell level.

FIGS. 10A-10F are micrographs which show that exposure of hESCs to nodal, activin A and activin B (NAA) yields a striking increase in the number of SOX17⁺ cells over the period of 5 days (A-C). By comparing to the relative abundance of SOX17⁺ cells to the total number of cells present in each field, as indicated by DAPI stained nuclei (D-F), it can be seen that approximately 30-50% of all cells are immunoreactive for SOX17 after five days treatment with NAA.

FIG. 11 is a bar chart which demonstrates that activin A (0, 10, 30 or 100 ng/ml) dose-dependently increases SOX17 gene expression in differentiating hESCs. Increased expression is already robust after 3 days of treatment on adherent cultures and continues through subsequent 1, 3 and 5 days of suspension culture as well.

FIGS. 12A-12C are bar charts which demonstrate the effect of activin A on the expression of MIXL1 (panel A), GATA4 (panel B) and HNF3b (panel C). Activin A dose-dependent increases are also observed for three other markers of definitive endoderm; MIXL1, GATA4 and HNF3b. The magnitudes of increased expression in response to activin dose are strikingly similar to those observed for SOX17, strongly indicating that activin A is specifying a population of cells that co-express all four genes (SOX17±, MIXL1+, GATA4⁺ and HNF3b⁺).

FIGS. 13A-13C are bar charts which demonstrate the effect of activin A on the expression of AFP (panel A), SOX7 (panel B) and SPARC (panel C). There is an activin A dose-dependent decrease in expression of the visceral endoderm marker AFP. Markers of primitive endoderm (50×7) and parietal endoderm (SPARC) remain either unchanged or exhibit suppression at some time points indicating that activin A does not act to specify these extra-embryonic endoderm cell types. This further supports the fact that the increased expression of SOX17, MIXL1, GATA4, and HNF3b are due to an increase in the number of definitive endoderm cells in response to activin A.

FIGS. 14A-14B are bar charts showing the effect of activin A on ZIC1 (panel A) and Brachyury expression (panel B) Consistent expression of the neural marker ZIC1 demonstrates that there is not a dose-dependent effect of activin A on neural differentiation. There is a notable suppression of mesoderm differentiation mediated by 100 ng/ml of activin A treatment as indicated by the decreased expression of brachyury. This is likely the result of the increased specification of definitive endoderm from the mesendoderm precursors. Lower levels of activin A treatment (10 and 30 ng/ml) maintain the expression of brachyury at later time points of differentiation relative to untreated control cultures.

FIGS. 15A-15B are micrographs showing decreased parietal endoderm differentiation in response to treatment with activins. Regions of TM^(im) parietal endoderm are found through the culture (A) when differentiated in serum alone, while differentiation to TM+cells is scarce when activins are included (B) and overall intensity of TM immunoreactivity is lower.

FIGS. 16A-16D are micrographs which show marker expression in response to treatment with activin A and activin B. hESCs were treated for four consecutive days with activin A and activin B and triple labeled with SOX17, AFP and TM antibodies. Panel A—SOX17; Panel B—AFP; Panel C—TM; and Panel D—Phase/DAPI. Notice the numerous SOX17 positive cells (A) associated with the complete absence of AFP (B) and TM (C) immunoreactivity.

FIG. 17 is a micrograph showing the appearance of definitive endoderm and visceral endoderm in vitro from hESCs. The regions of visceral endoderm are identified by AFP^(hi)/SOX17^(lo/−) while definitive endoderm displays the complete opposite profile, SOX17^(hi)/AFP^(lo/−). This field was selectively chosen due to the proximity of these two regions to each other. However, there are numerous times when SOX17^(hi)/AFp^(lo/−) regions are observed in absolute isolation from any regions of AFP^(hi) cells, suggesting the separate origination of the definitive endoderm cells from visceral endoderm cells.

FIG. 18 is a diagram depicting the TGFβ family of ligands and receptors. Factors activating AR Smads and BR Smads are useful in the production of definitive endoderm from human embryonic stem cells (see, J Cell Physiol.187:265-76).

FIG. 19 is a bar chart showing the induction of SOX17 expression over time as a result of treatment with individual and combinations of TGFβ factors.

FIG. 20 is a bar chart showing the increase in SOX17⁺ cell number with time as a result of treatment with combinations of TGFβ factors.

FIG. 21 is a bar chart showing induction of SOX17 expression over time as a result of treatment with combinations of TGFβ factors.

FIG. 22 is a bar chart showing that activin A induces a dose-dependent increase in SOX17⁺ cell number.

FIG. 23 is a bar chart showing that addition of Wnt3a to activin A and activin B treated cultures increases SOX17 expression above the levels induced by activin A and activin B alone.

FIGS. 24A-24C are bar charts showing differentiation to definitive endoderm is enhanced in low PBS conditions. Treatment of hESCs with activins A and B in media containing 2% FBS (2AA) yields a 2-3 times greater level of SOX17 expression as compared to the same treatment in 10% FBS media (10AA) (panel A). Induction of the definitive endoderm marker MIXL1 (panel B) is also affected in the same way and the suppression of AFP (visceral endoderm) (panel C) is greater in 2% FBS than in 10% FBS conditions.

FIGS. 25A-25D are micrographs which show SOX17⁺ cells are dividing in culture. SOX17 immunoreactive cells are present at the differentiating edge of an hESC colony (C, D) and are labeled with proliferating cell nuclear antigen (PCNA) (panel B) yet are not co-labeled with OCT4 (panel C). In addition, clear mitotic figures can be seen by DAPI labeling of nuclei in both SOX17⁺ cells (arrows) as well as OCT4+, undifferentiated hESCs (arrowheads) (D).

FIG. 26 is a bar chart showing the relative expression level of CXCR4 in differentiating hESCs under various media conditions.

FIGS. 27A-27D are bar charts that show how a panel of definitive endoderm markers share a very similar pattern of expression to CXCR4 across the same differentiation treatments displayed in FIG. 26 .

FIGS. 28A-28E are bar charts showing how markers for mesoderm (BRACHYURY, MOX1), ectoderm (SOX1, ZIC1) and visceral endoderm (50×7) exhibit an inverse relationship to CXCR4 expression across the same treatments displayed in FIG. 26 .

FIGS. 29A-29F are micrographs that show the relative difference in SOX17 immunoreactive cells across three of the media conditions displayed in FIGS. 26-28 .

FIGS. 30A-30C are flow cytometry dot plots that demonstrate the increase in CXCR4⁺ cell number with increasing concentration of activin A added to the differentiation media.

FIGS. 31A-31D are bar charts that show the CXCR4⁺ cells isolated from the high dose activin A treatment (A100-CX+) are even further enriched for definitive endoderm markers than the parent population (A100).

FIG. 32 is a bar chart showing gene expression from CXCR4⁺ and CXCR4⁻ cells isolated using fluorescence-activated cell sorting (FACS) as well as gene expression in the parent populations. This demonstrates that the CXCR4⁺ cells contain essentially all the CXCR4 gene expression present in each parent population and the CXCR4⁻populations contain very little or no CXCR4 gene expression.

FIGS. 33A-33D are bar charts that demonstrate the depletion of mesoderm (BRACHYURY, MOX1), ectoderm (ZIC1) and visceral endoderm (50×7) gene expression in the CXCR4⁺ cells isolated from the high dose activin A treatment which is already suppressed in expression of these non-definitive endoderm markers.

FIGS. 34A-34M are bar charts showing the expression patterns of marker genes that can be used to identify definitive endoderm cells. The expression analysis of definitive endoderm markers, FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1 is shown in panels G-L, respectively. The expression analysis of previously described lineage marking genes, SOX17, SOX7, SOX17/SOX7, TM, ZIC1, and MOX1 is shown in panels A-F, respectively. Panel M shows the expression analysis of CXCR4. With respect to each of panels A-M, the column labeled hESC indicates gene expression from purified human embryonic stem cells; 2NF indicates cells treated with 2% FBS, no activin addition; 0.1A100 indicates cells treated with 0.1% FBS, 100 ng/ml activin A; 1A100 indicates cells treated with 1% PBS, 100 ng/ml activin A; and 2A100 indicates cells treated with 2% FBS, 100 ng/ml activin A.

FIG. 35 is a chart which shows the relative expression of the PDX1 gene in a culture of hESCs after 4 days and 6 days with and without activin in the presence of retinoic acid (RA) and fibroblast growth factor (FGF-10) added on day 4.

FIGS. 36A-36F are charts which show the relative expression of marker genes in a culture of hESCs after 4 days and 6 days with and without activin in the presence of retinoic acid (RA) and fibroblast growth factor (FGF-10) added on day 4. The panels show the relative levels of expression of the following marker genes: (A) SOX17; (B) SOX7; (C) AFP; (D) SOX1; (E) ZIC1; and (F) NFM.

FIGS. 37A-37C are charts which show the relative expression of marker genes in a culture of hESCs after 4 days and 8 days with and without activin in the presence or absence of combinations of retinoic acid (RA), fibroblast growth factor (FGF-10) and fibroblast growth factor (FGF-4) added on day 4. The panels show the relative levels of expression of the following marker genes: (A) PDX1; (B) SOX7; and (C) NFM.

FIGS. 38A-38G are charts which show the relative expression of marker genes in a culture of definitive endoderm cells contacted with 50 ng/ml FGF-10 in combination with either 1 μM, 0.2 μM or 0.04 μM retinoic acid (RA) added on day 4. The panels show the relative levels of expression of the following marker genes: (A) PDX1; (B) HOXA3; (C) HOXC6; (D) HOXA13; (E) CDX1; (F) SOX1; and (G) NFM.

FIGS. 39A-39E are charts which show the relative expression of marker genes in a culture of hESCs after 4 days and 8 days with and without activin in the presence of combinations of retinoic acid (RA), fibroblast growth factor (FGF-10) and one of the following: serum replacement (SR), fetal bovine serum (FBS) or B27. The panels show the relative levels of expression of the following marker genes: (A) PDX1; (B) SOX7; (C) AFP; (D) ZIC1; and (E) NFM.

FIGS. 40A-40B are charts which show the relative expression of marker genes for pancreas (PDX1, HNF6) and liver (HNF6) in a culture of hESCs after 6 days (just prior to addition of RA) and at 9 days (three days after exposure to RA). Various conditions were included to compare the addition of activin B at doses of 10 ng/ml (a10), 25 ng/ml (a25) or 50 ng/ml (a50) in the presence of either 25 ng/ml (A25) or 50 ng/ml (A50) activin A. The condition without any activin A or activin B (NF) serves as the negative control for definitive endoderm and PDX1-positive endoderm production. The panels show the relative levels of expression of the following marker genes: (A) PDX1and (B) HNF6.

FIGS. 41A-41C are charts which show the relative expression of marker genes in a culture of hESCs with 100 ng/ml (A100), 50 ng/ml (A50) or without (NF) activin A at 5 days (just prior to retinoic acid addition) and at 2, 4, and 6 days after RA exposure (day 7, 9, and 11, respectively). The percentage label directly under each bar indicates the PBS dose during days 3-5 of differentiation. Starting at day 7, cells treated with RA (R) were grown in RPMI medium comprising 0.5% FBS. The RA concentration was 2 μM on day 7,1 μM on day 9 and 0.2 μM on day 11. The panels show the relative levels of expression of the following marker genes: (A) PDX1; (B) ZIC1; (C) SOX7.

FIGS. 42A-42B are charts which show the relative expression of marker genes in a culture of hESCs treated first with activin A in low FBS to induce definitive endoderm (day 5) and then with fresh (A25R) medium comprising 25 ng/ml activin A and RA or various conditioned media (MEFCM, CM#2, CM#3 and CM#4) and RA to induce PDX1-expressing endoderm. Marker expression was determined on days 5, 6, 7, 8 and 9. The panels show the relative levels of expression of the following marker genes: (A) PDX1; (B) CDX1.

FIG. 43 is a chart which shows the relative expression of PDX1 in a culture of hESCs treated first with activin A in low FBS to induce definitive endoderm and followed by fresh media comprising activin A and retinoic acid (A25R) or varying amounts of RA in conditioned media diluted into fresh media. Total volume of media is 5 ml in all cases.

FIG. 44 is a Western blot showing PDX1 immunoprecipitated from RA-treated definitive endoderm cells 3 days (d8) and 4 days (d9) after the addition of RA and 50 ng/ml activin A.

FIG. 45 is a summary chart displaying the results of a fluorescence-activated cell sort (FACs) of PDX1-positive foregut endoderm cells genetically tagged with a EGFP reporter under control of the PDX1 promoter.

FIG. 46 is a chart showing relative PDX1 expression levels normalized to housekeeping genes for sorted populations of live cells (Live), EGFP-negative cells (Neg) and EGFP-positive cells (GFP+).

FIG. 47 is a chart showing relative PDX1 expression levels normalized to housekeeping genes for sorted populations of live cells (Live), EGFP-negative cells (Neg), the half of the EGFP-positive cell population that has the lowest EGFP signal intensity (Lo) and the half of the EGFP-positive cell population that has the highest EGFP signal intensity (Hi).

FIGS. 48A-48E are a charts showing the relative expression levels normalized to housekeeping genes of five pancreatic endoderm markers in sorted populations of live cells (Live), EGFP-negative cells (Neg) and EGFP-positive cells (GFP+). Panels: A — NKX2.2; B — GLUT2; C — HNF313; D — KRT19 and E — HNF4oc.

FIGS. 49A-49B are charts showing the relative expression levels normalized to housekeeping genes of two non-pancreatic endoderm markers in sorted populations of live cells (Live), EGFP-negative cells (Neg) and EGFP-positive cells (GFP+). (A) ZIC1 and (B) GFAP.

FIGS. 50A-50D are charts showing the relative expression of marker genes in a culture of hESCs at the start of differentiation prior to addition of any factor (0 d), and either in the presence of 100 ng/ml activin A (A100) for 3 days (3 d) followed by 3 ng/ml BMP4 and 50 ng/ml FGF-10 (B3F50) on days 4-11 (7d, 9d and 11d) or in the presence of 100 ng/ml activin A (A100) for 5 days (5d) followed by 25 ng/ml activin A and 2 μM RA (A25R) on day 6 and 7 (7 d). The panels show the relative levels of expression of the following marker genes: (A) ALB; (B) PDX1; (C) HB9 and (D) HHEX.

FIGS. 51A-51D are charts showing the relative expression of marker genes in a culture of hESCs at the start of differentiation prior to addition of any factor (0 d), and after four days of differentiation under one of the four following conditions: (a) 100 ng/ml BMP4 and 5 μM SU5402 (B/SU); (b) no factor (NF); (c) 15 ng/ml activin A (A15); or (d) 100 ng/ml activin A. This differentiation is followed by incubation in the presence of 3 ng/ml BMP4, 50 ng/ml FGF-10 and 0.5 μM KAAD-cyclopamine (B3F50K0.5) on days 5-12 (6d, 8d, 10d and 12d). The panels show the relative levels of expression of the following marker genes: (A) CER; (B) SOX17; (C) PDX1 and (D) ALB.

FIGS. 52A-52B are charts showing the relative expression of marker genes in a culture of hESCs at the start of differentiation prior to addition of any factor (0 d); in the presence of 100 ng/ml activin A (A100) for 3 days (3 d); in the presence of no factor (NF), 50 ng/ml FGF-10 and 0.5 μM KAAD-cyclopamine (FK) or 3 ng/ml BMP4, 50 ng/ml FGF-10 and 0.5 μM KAAD-cyclopamine (BFK) on days 4 and 5 (5d); and in the presence of no factor in RPMI medium (2R), no factor in RPMI medium supplemented with B27 (ORB), no factor in CMRL medium supplemented with B27 (OCB), 50 ng/ml FGF-10 and 0.5 μM KAAD-cyclopamine in CMRL medium supplemented with B27 (FK) or 3 ng/ml BMP4, 50 ng/ml FGF-10 and 0.5 μM KAAD-cyclopamine in CMRL medium supplemented with B27 (BFK) on days 6-13 (7d, 9d, lld and 13d). The panels show the relative levels of expression of the following marker genes: (A) PDX1 and (B) ALB.

FIGS. 53A-53E are charts showing the relative expression of marker genes in a culture of hESCs at the start of differentiation prior to addition of any factor (0 d), and either in the presence of 100 ng/ml activin A (A100) for 3 days (3 d) followed by 3 ng/ml BMP4 and 50 ng/ml FGF-10 (B3F50) on days 4-11 (7d, 9d and 11d) or in the presence of 100 ng/ml activin A (A100) for 5 days (5d) followed by 25 ng/ml activin A and 2 μM RA (A25R) on day 6 and 7 (7 d). The panels show the relative levels of expression of the following marker genes: (A) PDX1; (B) SERPINF2; (C) DUSP9; (D) CDH6 and (E) SOX9.

FIGS. 54A-54D are charts showing the relative expression of marker genes in a culture of hESCs at the start of differentiation prior to addition of any factor (0 d), and either in the presence of 100 ng/ml activin A (A100) for 3 days (3 d) followed by 3 ng/ml BMP4 and 50 ng/ml FGF-10 (B3F50) on days 4-11 (7d, 9d and 11d) or in the presence of 100 ng/ml activin A

(A100) for 5 days (5d) followed by 25 ng/ml activin A and 2 μM RA (A25R) on day 6 and 7 (7 d). The panels show the relative levels of expression of the following marker genes: (A) HOXA1; (B) PDE11A; (C) FAM49A and (D) WNTSA.

Sequence Listing

The Sequence Listing is submitted in xml format as 9511-96324-05_Sequence_Listing.xml, Jul. 19, 2022, 4,431 bytes, which is incorporated by reference herein.

DETAILED DESCRIPTION

A crucial stage in early human development termed gastrulation occurs 2-3 weeks after fertilization. Gastrulation is extremely significant because it is at this time that the three primary germ layers are first specified and organized (Lu et al., 2001; Schoenwolf and Smith, 2000). The ectoderm is responsible for the eventual formation of the outer coverings of the body and the entire nervous system whereas the heart, blood, bone, skeletal muscle and other connective tissues are derived from the mesoderm. Definitive endoderm is defined as the germ layer that is responsible for formation of the entire gut tube which includes the esophagus, stomach and small and large intestines, and the organs which derive from the gut tube such as the lungs, liver, thymus, parathyroid and thyroid glands, gall bladder and pancreas (Grapin-Botton and Melton, 2000; Kimelman and Griffin, 2000; Tremblay et al., 2000; Wells and Melton, 1999; Wells and Melton, 2000). A very important distinction should be made between the definitive endoderm and the completely separate lineage of cells termed primitive endoderm. The primitive endoderm is primarily responsible for formation of extra-embryonic tissues, mainly the parietal and visceral endoderm portions of the placental yolk sac and the extracellular matrix material of Reichert's membrane. During gastrulation, the process of definitive endoderm formation begins with a cellular migration event in which mesendoderm cells (cells competent to form mesoderm or endoderm) migrate through a structure called the primitive streak. Definitive endoderm is derived from cells, which migrate through the anterior portion of the streak and through the node (a specialized structure at the anterior-most region of the streak). As migration occurs, definitive endoderm populates first the most anterior gut tube and culminates with the formation of the posterior end of the gut tube.

The PDX1 Gene Expression During Development

PDX1 (also called STF-1, IDX-1, IPF-1, IUF-1 and GSF) is a transcription factor that is necessary for development of the pancreas and rostral duodenum. PDX1 is first expressed in the pancreatic endoderm, which arises from posterior foregut endoderm and will produce both the exocrine and endocrine cells, starting at E8.5 in the mouse. Later, PDX1 becomes restricted to beta-cells and some delta-cells. This expression pattern is maintained in the adult. PDX1 is also expressed in duodenal endoderm early in development, which is adjacent to the forming pancreas, then in the duodenal enterocytes and enteroendocrine cells, antral stomach and in the common bile, cystic and biliary ducts. This region of expression also becomes limited, at the time that pancreatic expression becomes restricted, to predominantly the rostral duodenum.

Targeted disruption of the PDX1 gene in mouse and man leads to pancreatic agenesis (Jonsson, J., et al., Nature, 606-609, 1994; Offield, MF, et al. Devel. 983-995, 1996; Stoffers, D.A., et al. Nature Genetics, 106-110, 1997). PDX1 is also required during terminal differentiation of the insulin and somatostatin pancreatic endocrine cells and functional disruption of a single allele in humans is associated with severe pancreatic dysfunction of MODY type 4 (maturity onset diabetes of the young) and late onset type II diabetes (Stoffers D. A., et al. Nature Genetics 138-139, 1997).

During embryogenesis of the pancreas a budding of the prospective pancreatic tissue occurs on both the dorsal and ventral side of the primitive gut endoderm. These protrusions occur in a regionally defined manner at the most posterior end of the foregut endoderm. In mice this occurs at approximately 8.5-9.5 days post conception (dpc) and in humans at 30 dpc. By 35 dpc in the human, the ventral and dorsal buds have grown, developed a branched ductal system and fused to form the definitive organ. PDX1 protein is required for the early pancreatic buds to expand and differentiate into the principal cells comprising the pancreas which include duct, acinar and endocrine cells.

Due to their locations on opposite sides of the gut tube and their respective associations with notochord and cardiac mesoderm the developmental programs for the dorsal and ventral pancreatic structures are distinctly different. With regard to the unique developmental programs controlling specification of the dorsal and ventral pancreatic anlaga we have developed two separate methodologies for producing dorsally-biased and ventrally-biased PDX1-expressing foregut endoderm from definitive endoderm (DE) cultures generated from human embryonic stem cells (hESCs). These PDX1-expressing (PDX1-positive) foregut endoderm cells are competent to develop into pancreatic and duodenal epithelium as well as endocrine cells of the anterior gastric mucosa.

Aspects of the present invention relate to the discovery that definitive endoderm cells can be differentiated into at least two distinguishable types of PDX1-expressing (PDX1-positive) foregut endoderm cells. We have also discovered that prior to the expression of PDX1, definitive endoderm cells can be differentiated into a PDX1-negative foregut endoderm cell. Providing these PDX1-negative cells with a retinoid compound, such as retinoic acid, induces the expression of PDX1. In another aspect of the present invention, definitive endoderm cells are differentiated to form dorsal PDX1-positive foregut endoderm cells. As used herein, with respect to PDX1-positive foregut endoderm, “dorsal” or “dorsally-biased” means that the PDX1-positive foregut endoderm cells are those that can give rise to tissues derived from the dorsal side of the posterior portion of the foregut, such as the dorsal pancreatic bud. Once a PDX1-positive foregut endoderm cell becomes “dorsally-biased” it does not typically develop into tissues derived from the ventral side of the posterior portion of the foregut. In another aspect, definitive endoderm cells are differentiated to form ventral PDX1-positive foregut endoderm cells. As used herein, with respect to PDX1-positive foregut endoderm, “ventral” or “ventrally-biased” means that the PDX1-positive foregut endoderm cells are those that can give rise to tissues derived from the ventral side of the posterior portion of the foregut, such as the liver and the ventral pancreatic bud. Once a PDX1-positive foregut endoderm cell becomes “ventrally-biased” it does not typically develop into tissues derived from the dorsal side of the posterior portion of the foregut.

In view of the foregoing discovery, embodiments of the present invention relate to compositions of PDX1-negative foregut endoerm cells, dorsally-biased PDX1-positive foregut endoderm cells, ventrally-biased PDX1-positive foregut endoderm cells and/or compositions comprising mixtures of dorsally-biased and ventrally-biased PDX1-positive foregut endoderm cells as well as methods for the production of such compositions. Other embodiments of the present invention relate to screening of PDX1-negative foregut endoderm cells for factors that promote the differentiation of such cells. Still other embodiments relate to screening dorsal, ventral or mixed populations of PDX1-positive foregut endoderm cells for factors that promote the differentiation of such cells. By “mixed populations” is meant a cell population comprising significant amounts of both dorsal PDX1-positive foregut endoderm cells and ventral PDX1-positive foregut endoderm cells.

As used herein, FGF-family growth factor includes, but is not limited to, FGF-family growth factor selected from the group consisting of FGF1, FGF2, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGF10, FGF11, FGF12, FGF13, FGF14, FGF15, FGF16, FGF17, FGF18, FGF19, FGF20, FGF21, FGF22 and/or FGF23.

As used herein, hedgehog inhibitor includes, but is not limited to, KKAD-cyclopamine, KKAD-cyclopamine analogs, jervine, jervine analogs, hedgehog pathway blocking antibodies and any other inhibitors of hedgehog pathway function known to those of ordinary skill in the art.

PDX1-Negative Foregut Endoderm Cells and Processes Related Thereto

Embodiments of the present invention relate to novel, defined processes for the production of PDX1-negative endoderm cells, wherein the PDX1-negative endoderm cells are multipotent cells that can differentiate into cells, tissues or organs derived from the foregut/midgut region of the gut tube (PDX1-negative foregut/midgut endoderm). As used herein, “multipotent” or “multipotent cell” refers to a cell type that can give rise to a limited number of other particular cell types but which cannot give rise to all three primary embryonic cells lineages (endoderm, ectoderm and mesoderm). As used herein, “foregut/midgut” refers to cells of the anterior portion of the gut tube as well as cells of the middle portion of the gut tube, including cells of the foregut/midgut junction.

Some preferred embodiments of the present invention relate to processes for the production of PDX1-negative foregut endoderm cells. In some embodiments, these PDX1-negative foregut endoderm cells are multipotent cells that can differentiate into cells, tissues or organs derived from the anterior portion of the gut tube (PDX1-negative foregut endoderm).

Dorsal, Ventral and Mixed Populations of PDX1-Positive Foregut Endoderm Cells and Processes Related Thereto

Embodiments of the present invention relate to novel, defined processes for the production of PDX1-negative endoderm cells, wherein the PDX1-positive endoderm cells are multipotent cells that can differentiate into cells, tissues or organs derived from the foregut/midgut region of the gut tube (PDX1-positive foregut/midgut endoderm). Other embodiments of the present invention relate to novel, defined processes for the production of PDX1-positive endoderm cells, wherein the PDX1-positive endoderm cells are multipotent cells that can differentiate into cells, tissues or organs derived from the foregut/midgut region of the gut tube (PDX1-positive foregut/midgut endoderm). As used herein, “multipotent” or “multipotent cell” refers to a cell type that can give rise to a limited number of other particular cell types but which cannot give rise to all three primary embryonic cells lineages (endoderm, ectoderm and mesoderm). As used herein, “foregut/midgut” refers to cells of the anterior portion of the gut tube as well as cells of the middle portion of the gut tube, including cells of the foregut/midgut junction. In some embodiments, the PDX1 positive endoderm cells are dorsal foregut endoderm cells. In other embodiments, the PDX1 positive endoderm cells are ventral foregut endoderm cells.

Some preferred embodiments of the present invention relate to processes for the production of PDX1-positive foregut endoderm cells. In some embodiments, these PDX1-positive foregut endoderm cells are multipotent cells that can differentiate into cells, tissues or organs derived from the anterior portion of the gut tube (PDX1-positive foregut endoderm). In some embodiments, the PDX1 positive endoderm cells are dorsal foregut endoderm cells. In other embodiments, the PDX1 positive endoderm cells are ventral foregut endoderm cells.

Additional preferred embodiments relate to processes for the production of PDX1-positive endoderm cells of the posterior portion of the foregut. In some embodiments, these PDX1-positive endoderm cells are multipotent cells that can differentiate into cells, tissues or organs derived from the posterior portion of the foregut region of the gut tube. In some embodiments, the PDX1 positive endoderm cells are dorsal endoderm cells that can differentiate into cells, tissues or organs derived from the posterior portion of the foregut, such as cells of the dorsal pancreatic bud. In other embodiments, the PDX1 positive endoderm cells are ventral foregut endoderm cells that can differentiate into cells, tissues or organs derived from the posterior portion of the foregut, such as cells of the ventral pancreatic bud.

The dorsal and/or ventral PDX1-positive foregut endoderm cells, such as those produced according to the methods described herein, can be used to produce fully differentiated insulin-producing β-cells. In some embodiments of the present invention, positive dorsal and/or ventral PDX1-foregut endoderm cells are produced by differentiating definitive endoderm cells that do not substantially express PDX1 (PDX1-negative definitive endoderm cells; also referred to herein as definitive endoderm) so as to form positive dorsal and/or ventral PDX1-positive foregut endoderm cells. PDX1-negative definitive endoderm cells can be prepared by differentiating pluripotent cells, such as embryonic stem cells, as described herein or by any other known methods. A convenient and highly efficient method for producing PDX1-negative definitive endoderm from pluripotent cells is described in U.S. patent Ser. No. 11/021,618, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2004, the disclosure of which is incorporated herein by reference in its entirety.

Processes of producing PDX1-positive foregut endoderm cells, including dorsal and/or ventral PDX1-positive foregut endoderm cells, provide a basis for efficient production of pancreatic tissues such as acinar cells, ductal cells and islet cells from pluripotent cells. In certain preferred embodiments, human dorsal and/or ventral PDX1-positive foregut endoderm cells are derived from human PDX1-negative definitive endoderm cells, which in turn, are derived from hESCs. These human dorsal and/or ventral PDX1-positive foregut endoderm cells can then be used to produce functional insulin-producing β-cells. To obtain useful quantities of insulin-producing β-cells, high efficiency of differentiation is desirable for each of the differentiation steps that occur prior to reaching the pancreatic islet/β-cell fate. Because differentiation of PDX1-negative definitive endoderm cells to dorsal and/or ventral PDX1-positive foregut endoderm cells represents an early step towards the production of functional pancreatic islet/β-cells (as shown in FIG. 1 ), high efficiency of differentiation at this step is particularly desirable.

In view of the desirability of efficient differentiation of PDX1-negative definitive endoderm cells to PDX1-positive foregut endoderm cells, some aspects of the present invention relate to in vitro methodology that results in approximately 2-25% conversion of PDX1-negative definitive endoderm cells to PDX1-positive foregut endoderm cells. Some aspects of the present invention relate to in vitro methodology that results in approximately 26% to at least approximately 75% conversion of PDX1-negative definitive endoderm cells to dorsal PDX1-positive foregut endoderm cells. Other aspects of the present invention relate to in vitro methodology that results in approximately 26% to at least approximately 75% conversion of PDX1-negative definitive endoderm cells to ventral PDX1-positive foregut endoderm cells. Typically, the above-described methods encompass the application of culture and growth factor conditions in a defined and temporally specified fashion. Further enrichment of the cell population for PDX1-positive foregut endoderm cells, including dorsal and/or ventral PDX1-positive foregut endoderm cells, can be achieved by isolation and/or purification of the PDX1-positive foregut endoderm cells from other cells in the population by using a reagent that specifically binds to the PDX1-positive foregut endoderm cells. As an alternative, PDX1-positive foregut endoderm cells, including dorsal and/or ventral PDX1-positive foregut endoderm cells, can be labeled with a reporter gene, such as green fluorescent protein (GFP), so as to enable the detection of PDX1 expression. Such fluorescently labeled cells can then be purified by fluorescent activated cell sorting (FACS). Further aspects of the present invention relate to cell cultures and enriched cell populations comprising PDX1-positive foregut endoderm cells as well as methods for identifying factors useful in the differentiation to and from PDX1-positive foregut endoderm. Additional aspects of the present invention relate to cell cultures and enriched cell populations comprising dorsal PDX1-positive foregut endoderm cells as well as methods for identifying factors useful in the differentiation to and from dorsal PDX1-positive foregut endoderm. Still other aspects of the present invention relate to cell cultures and enriched cell populations comprising ventral PDX1-positive foregut endoderm cells as well as methods for identifying factors useful in the differentiation to and from ventral PDX1-positive foregut endoderm.

In order to determine the amount of PDX1-positive foregut endoderm cells in a cell culture or cell population, a method of distinguishing this cell type from the other cells in the culture or in the population is desirable. Accordingly, certain embodiments of the present invention relate to cell markers whose presence, absence and/or relative expression levels are indicative of PDX1-positive foregut endoderm cells, including dorsal and/or ventral PDX1-positive foregut endoderm cells, as well as methods for detecting and determining the expression of such markers. As used herein, “expression” refers to the production of a material or substance as well as the level or amount of production of a material or substance. Thus, determining the expression of a specific marker refers to detecting either the relative or absolute amount of the marker that is expressed or simply detecting the presence or absence of the marker. As used herein, “marker” refers to any molecule that can be observed or detected. For example, a marker can include, but is not limited to, a nucleic acid, such as a transcript of a specific gene, a polypeptide product of a gene, a non-gene product polypeptide, a glycoprotein, a carbohydrate, a glycolipd, a lipid, a lipoprotein or a small molecule (for example, molecules having a molecular weight of less than 10,000 amu).

In some embodiments of the present invention, the presence, absence and/or level of expression of a marker is determined by quantitative PCR (Q-PCR). For example, the amount of transcript produced by certain genetic markers, such as PDX1, SOX17, SOX7, SOX1, ZIC1, NFM, alpha-fetoprotein (AFP), homeobox A13 (HOXA13), homeobox C6 (HOXC6), and/or other markers described herein is determined by Q-PCR. In other embodiments, immunohistochemistry is used to detect the proteins expressed by the above-mentioned genes. In still other embodiments, Q-PCR and immunohistochemical techniques are both used to identify and determine the amount or relative proportions of such markers. In some embodiments, markers that are common to both dorsal and ventral PDX1-positive foregut endoderm cells, such as PDX1 and/or one or more markers selected from Table 3, are detected by Q-PCR and/or immunohistochemistry. In other embodiments, markers that are preferentially, specifically or uniquely expressed in dorsal PDX1-positive foregut endoderm cells, such as one or more markers selected from Table 4, are detected by Q-PCR and/or immunohistochemistry.

By using the differentiation and detection methods described herein, it is possible to identify PDX1-positive foregut endoderm cells, including dorsal and/or ventral PDX1-positive foregut endoderm cells, as well as determine the proportion of dorsal and/or ventral PDX1-positive foregut endoderm cells in a cell culture or cell population. For example, in some embodiments of the present invention, the dorsal and/or ventral PDX1-positive foregut endoderm cells or cell populations that are produced express the PDX1 gene at a level of at least about 2 orders of magnitude greater than PDX1-negative cells or cell populations. In other embodiments, the dorsal and/or ventral PDX1-positive foregut endoderm cells and cell populations that are produced express the PDX1 gene at a level of more than 2 orders of magnitude greater than PDX1-negative cells or cell populations. In still other embodiments, the dorsal and/or ventral PDX1-positive foregut endoderm cells or cell populations that are produced express one or more of the markers selected from the group consisting of PDX1, SOX17, HOXA13 and HOXC6 at a level of about 2 or more than 2 orders of magnitude greater than PDX1-negative definitive endoderm cells or cell populations. In yet other embodiments, the dorsal and/or ventral PDX1-positive foregut endoderm cells or cell populations that are produced express one or more of the markers selected from Table 3 at a level of about 2 or more than 2 orders of magnitude greater than PDX1-negative definitive endoderm cells or cell populations. In further embodiments, the dorsal PDX1-positive foregut endoderm cells or cell populations that are produced express one or more of the markers selected from Table 4 at a level of about 2 or more than 2 orders of magnitude greater than PDX1-negative definitive endoderm cells or cell populations.

The compositions and methods described herein have several useful features. For example, the cell cultures and cell populations comprising PDX1-positive endoderm, including dorsal and/or ventral PDX1-positive foregut endoderm, as well as the methods for producing such cell cultures and cell populations, are useful for modeling the early stages of human development. Furthermore, the compositions and methods described herein can also serve for therapeutic intervention in disease states, such as diabetes mellitus. For example, since PDX1-positive foregut endoderm serves as the source for only a limited number of tissues, it can be used in the development of pure tissue or cell types.

Production of PDX1-Negative Definitive Endoderm (Definitive Endoderm) from Pluripotent Cells

Cell cultures and/or cell populations comprising PDX1-positive foregut endoderm cells are produced from pluripotent cells by first producing PDX1-negative definitive endoderm (also referred to as “definitive endoderm”). Processes for differentiating pluripotent cells to produce cell cultures and enriched cell populations comprising definitive endoderm is described briefly below and in detail in U.S. patent Ser. No. 11/021,618, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2004, the disclosure of which is incorporated herein by reference in its entirety. In some of these processes, the pluripotent cells used as starting material are stem cells. In certain processes, definitive endoderm cell cultures and enriched cell populations comprising definitive endoderm cells are produced from embryonic stem cells. As used herein, “embryonic” refers to a range of developmental stages of an organism beginning with a single zygote and ending with a multicellular structure that no longer comprises pluripotent or totipotent cells other than developed gametic cells. In addition to embryos derived by gamete fusion, the term “embryonic” refers to embryos derived by somatic cell nuclear transfer. A preferred method for deriving definitive endoderm cells utilizes human embryonic stem cells as the starting material for definitive endoderm production. Such pluripotent cells can be cells that originate from the morula, embryonic inner cell mass or those obtained from embryonic gonadal ridges. Human embryonic stem cells can be maintained in culture in a pluripotent state without substantial differentiation using methods that are known in the art. Such methods are described, for example, in U.S. Pat. Nos. 5,453,357, 5,670,372, 5,690,926 5,843,780, 6,200,806 and 6,251,671 the disclosures of which are incorporated herein by reference in their entireties.

In some processes for producing definitive endoderm cells, hESCs are maintained on a feeder layer. In such processes, any feeder layer which allows hESCs to be maintained in a pluripotent state can be used. One commonly used feeder layer for the cultivation of human embryonic stem cells is a layer of mouse fibroblasts. More recently, human fibroblast feeder layers have been developed for use in the cultivation of hESCs (see US Patent Application No. 2002/0072117, the disclosure of which is incorporated herein by reference in its entirety). Alternative processes for producing definitive endoderm permit the maintenance of pluripotent hESC without the use of a feeder layer. Methods of maintaining pluripotent hESCs under feeder-free conditions have been described in US Patent Application No. 2003/0175956, the disclosure of which is incorporated herein by reference in its entirety.

The human embryonic stem cells used herein can be maintained in culture either with or without serum. In some embryonic stem cell maintenance procedures, serum replacement is used. In others, serum free culture techniques, such as those described in US Patent Application No. 2003/0190748, the disclosure of which is incorporated herein by reference in its entirety, are used.

Stem cells are maintained in culture in a pluripotent state by routine passage until it is desired that they be differentiated into definitive endoderm. In some processes, differentiation to definitive endoderm is achieved by providing to the stem cell culture a growth factor of the TGFβ superfamily in an amount sufficient to promote differentiation to definitive endoderm. Growth factors of the TGFβ superfamily which are useful for the production of definitive endoderm are selected from the Nodal/Activin or BMP subgroups. In some preferred differentiation processes, the growth factor is selected from the group consisting of Nodal, activin A, activin B and BMP4. Additionally, the growth factor Wnt3a and other Wnt family members are useful for the production of definitive endoderm cells. In certain differentiation processes, combinations of any of the above-mentioned growth factors can be used.

With respect to some of the processes for the differentiation of pluripotent stem cells to definitive endoderm cells, the above-mentioned growth factors are provided to the cells so that the growth factors are present in the cultures at concentrations sufficient to promote differentiation of at least a portion of the stem cells to definitive endoderm cells. In some processes, the above-mentioned growth factors are present in the cell culture at a concentration of at least about 5 ng/ml, at least about 10 ng/ml, at least about 25 ng/ml, at least about 50 ng/ml, at least about 75 ng/ml, at least about 100 ng/ml, at least about 200 ng/ml, at least about 300 ng/ml, at least about 400 ng/ml, at least about 500 ng/ml, at least about 1000 ng/ml, at least about 2000 ng/ml, at least about 3000 ng/ml, at least about 4000 ng/ml, at least about 5000 ng/ml or more than about 5000 ng/ml.

In certain processes for the differentiation of pluripotent stem cells to definitive endoderm cells, the above-mentioned growth factors are removed from the cell culture subsequent to their addition. For example, the growth factors can be removed within about one day, about two days, about three days, about four days, about five days, about six days, about seven days, about eight days, about nine days or about ten days after their addition. In a preferred processes, the growth factors are removed about four days after their addition.

Cultures of definitive endoderm cells can be grown in medium containing reduced serum or no serum. Under certain culture conditions, serum concentrations can range from about 0.05% v/v to about 20% v/v. For example, in some differentiation processes, the serum concentration of the medium can be less than about 0.05% (v/v), less than about 0.1% (v/v), less than about 0.2% (v/v), less than about 0.3% (v/v), less than about 0.4% (v/v), less than about 0.5% (v/v), less than about 0.6% (v/v), less than about 0.7% (v/v), less than about 0.8% (v/v), less than about 0.9% (v/v), less than about 1% (v/v), less than about 2% (v/v), less than about 3% (v/v), less than about 4% (v/v), less than about 5% (v/v), less than about 6% (v/v), less than about 7% (v/v), less than about 8% (v/v), less than about 9% (v/v), less than about 10% (v/v), less than about 15% (v/v) or less than about 20% (v/v). In some processes, definitive endoderm cells are grown without serum or with serum replacement. In still other processes, definitive endoderm cells are grown in the presence of B27. In such processes, the concentration of B27 supplement can range from about 0.1% v/v to about 20% v/v.

Monitoring the Differentiation of Pluripotent Cells to PDX1-Negative Definitive Endoderm (Definitive Endoderm)

The progression of the hESC culture to definitive endoderm can be monitored by determining the expression of markers characteristic of definitive endoderm. In some processes, the expression of certain markers is determined by detecting the presence or absence of the marker. Alternatively, the expression of certain markers can be determined by measuring the level at which the marker is present in the cells of the cell culture or cell population. In such processes, the measurement of marker expression can be qualitative or quantitative. One method of quantitating the expression of markers that are produced by marker genes is through the use of quantitative PCR (Q-PCR). Methods of performing Q-PCR are well known in the art. Other methods which are known in the art can also be used to quantitate marker gene expression. For example, the expression of a marker gene product can be detected by using antibodies specific for the marker gene product of interest. In certain processes, the expression of marker genes characteristic of definitive endoderm as well as the lack of significant expression of marker genes characteristic of hESCs and other cell types is determined.

As described further in the Examples below, a reliable marker of definitive endoderm is the SOX17 gene. As such, the definitive endoderm cells produced by the processes described herein express the SOX17 marker gene, thereby producing the SOX17 gene product. Other markers of definitive endoderm are MIXL1, GATA4, HNF3b, GSC, FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1. Since definitive endoderm cells express the SOX17 marker gene at a level higher than that of the SOX7 marker gene, which is characteristic of primitive and visceral endoderm (see Table 1), in some processes, the expression of both SOX17 and SOX7 is monitored. In other processes, expression of the both the SOX17 marker gene and the OCT4 marker gene, which is characteristic of hESCs, is monitored. Additionally, because definitive endoderm cells express the SOX17 marker gene at a level higher than that of the AFP, SPARC or Thrombomodulin (TM) marker genes, the expression of these genes can also be monitored.

Another marker of definitive endoderm is the CXCR4 gene. The CXCR4 gene encodes a cell surface chemokine receptor whose ligand is the chemoattractant SDF-1. The principal roles of the CXCR4 receptor-bearing cells in the adult are believed to be the migration of hematopoetic cells to the bone marrow, lymphocyte trafficking and the differentiation of various B cell and macrophage blood cell lineages [Kim, C , and Broxmeyer, H. J. Leukocyte Biol. 65, 6-15 (1999)]. The CXCR4 receptor also functions as a coreceptor for the entry of HIV-1 into T-cells [Feng, Y., et al. Science, 272, 872-877 (1996)]. In an extensive series of studies carried out by [McGrath, K.E. et al. Dev. Biology 213, 442-456 (1999)], the expression of the chemokine receptor CXCR4 and its unique ligand, SDF-1 [Kim, C., and Broxmyer, H., J. Leukocyte Biol. 65, 6-15 (1999)], were delineated during early development and adult life in the mouse. The CXCR4/SDF1 interaction in development became apparent when it was demonstrated that if either gene was disrupted in transgenic mice [Nagasawa et al. Nature, 382, 635-638 (1996)], Ma, Q., et al Immunity, 10, 463-471 (1999)] it resulted in late embryonic lethality. McGrath et al. demonstrated that CXCR4 is the most abundant chemokine receptor messenger RNA detected during early gastrulating embryos (E7.5) using a combination of RNase protection and in situ hybridization methodologies. In the gastrulating embryo, CXCR4/SDF-1 signaling appears to be mainly involved in inducing migration of primitive-streak germlayer cells and is expressed on definitive endoderm, mesoderm and extraembryonic mesoderm present at this time. In E7.2-7.8 mouse embryos, CXCR4 and alpha-fetoprotein are mutually exclusive indicating a lack of expression in visceral endoderm [McGrath, K.E. et al. Dev. Biology 213, 442-456 (1999)].

Since definitive endoderm cells produced by differentiating pluripotent cells express the CXCR4 marker gene, expression of CXCR4 can be monitored in order to track the production of definitive endoderm cells. Additionally, definitive endoderm cells produced by the methods described herein express other markers of definitive endoderm including, but not limited to, SOX17, MIXL1, GATA4, HNF3b, GSC, FGF17, VWF, CALCR, FOXQ1, CMKOR1 and CRIP1. Since definitive endoderm cells express the CXCR4 marker gene at a level higher than that of the SOX7 marker gene, the expression of both CXCR4 and SOX7 can be monitored. In other processes, expression of the both the CXCR4 marker gene and the OCT4 marker gene, is monitored. Additionally, because definitive endoderm cells express the CXCR4 marker gene at a level higher than that of the AFP, SPARC or Thrombomodulin (TM) marker genes, the expression of these genes can also be monitored.

It will be appreciated that expression of CXCR4 in endodermal cells does not preclude the expression of SOX17. As such, definitive endoderm cells produced by the processes described herein will substantially express SOX17 and CXCR4 but will not substantially express AFP, TM, SPARC or PDX1.

Enrichment, Isolation and/or Purification of Definitive Endoderm

Definitive endoderm cells produced by any of the above-described processes can be enriched, isolated and/or purified by using an affinity tag that is specific for such cells. Examples of affinity tags specific for definitive endoderm cells are antibodies, ligands or other binding agents that are specific to a marker molecule, such as a polypeptide, that is present on the cell surface of definitive endoderm cells but which is not substantially present on other cell types that would be found in a cell culture produced by the methods described herein. In some processes, an antibody which binds to CXCR4 is used as an affinity tag for the enrichment, isolation or purification of definitive endoderm cells. In other processes, the chemokine SDF-1 or other molecules based on SDF-1 can also be used as affinity tags. Such molecules include, but not limited to, SDF-1 fragments, SDF-1 fusions or SDF-1 mimetics.

Methods for making antibodies and using them for cell isolation are known in the art and such methods can be implemented for use with the antibodies and definitive endoderm cells described herein. In one process, an antibody which binds to CXCR4 is attached to a magnetic bead and then allowed to bind to definitive endoderm cells in a cell culture which has been enzymatically treated to reduce intercellular and substrate adhesion. The cell/antibody/bead complexes are then exposed to a movable magnetic field which is used to separate bead-bound definitive endoderm cells from unbound cells. Once the definitive endoderm cells are physically separated from other cells in culture, the antibody binding is disrupted and the cells are replated in appropriate tissue culture medium.

Additional methods for obtaining enriched, isolated or purified definitive endoderm cell cultures or populations can also be used. For example, in some embodiments, the CXCR4 antibody is incubated with a definitive endoderm-containing cell culture that has been treated to reduce intercellular and substrate adhesion. The cells are then washed, centrifuged and resuspended. The cell suspension is then incubated with a secondary antibody, such as an FITC-conjugated antibody that is capable of binding to the primary antibody. The cells are then washed, centrifuged and resuspended in buffer. The cell suspension is then analyzed and sorted using a fluorescence activated cell sorter (FACS). CXCR4-positive cells are collected separately from CXCR4-negative cells, thereby resulting in the isolation of such cell types. If desired, the isolated cell compositions can be further purified by using an alternate affinity-based method or by additional rounds of sorting using the same or different markers that are specific for definitive endoderm.

In still other processes, definitive endoderm cells are enriched, isolated and/or purified using a ligand or other molecule that binds to CXCR4. In some processes, the molecule is SDF-1 or a fragment, fusion or mimetic thereof.

In preferred processes, definitive endoderm cells are enriched, isolated and/or purified from other non-definitive endoderm cells after the stem cell cultures are induced to differentiate towards the definitive endoderm lineage. It will be appreciated that the above-described enrichment, isolation and purification procedures can be used with such cultures at any stage of differentiation.

In addition to the procedures just described, definitive endoderm cells may also be isolated by other techniques for cell isolation. Additionally, definitive endoderm cells may also be enriched or isolated by methods of serial subculture in growth conditions which promote the selective survival or selective expansion of the definitive endoderm cells.

Using the methods described herein, enriched, isolated and/or purified populations of definitive endoderm cells and or tissues can be produced in vitro from pluripotent cell cultures or cell populations, such as stem cell cultures or populations, which have undergone at least some differentiation. In some methods, the cells undergo random differentiation. In a preferred method, however, the cells are directed to differentiate primarily into definitive endoderm. Some preferred enrichment, isolation and/or purification methods relate to the in vitro production of definitive endoderm from human embryonic stem cells. Using the methods described herein, cell populations or cell cultures can be enriched in definitive endoderm content by at least about 2- to about 1000-fold as compared to untreated cell populations or cell cultures.

Compositions Comprising PDX1-Negative Definitive Endoderm (Definitive Endoderm)

Cell compositions produced by the above-described methods include cell cultures comprising definitive endoderm and cell populations enriched in definitive endoderm. For example, cell cultures which comprise definitive endoderm cells, wherein at least about 50-80% of the cells in culture are definitive endoderm cells, can be produced. Because the efficiency of the differentiation process can be adjusted by modifying certain parameters, which include but are not limited to, cell growth conditions, growth factor concentrations and the timing of culture steps, the differentiation procedures described herein can result in about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or greater than about 95% conversion of pluripotent cells to definitive endoderm. In processes in which isolation of definitive endoderm cells is employed, for example, by using an affinity reagent that binds to the CXCR4 receptor, a substantially pure definitive endoderm cell population can be recovered.

Production of PDX1-Negative Foregut Endoderm

Definitive endoderm cells can be specified toward pancreatic differentiation by further differentiation of these cells to produce PDX1-negative foregut endoderm cells. In some of the differentiation processes described herein, cell cultures as well as enriched or purified cell populations comprising definitive endoderm cells can be used for further differentiation to cell cultures and/or enriched cell populations comprising PDX1-negative foregut endoderm cells.

Typically, definitive endoderm cells are differentiated to PDX1-negative foregut endoderm cells by reducing or eliminating TGFβ superfamily growth factor signaling in a cell culture or cell population of SOX17-positive definitive endoderm cells. In some embodiments, reducing or eliminating TGFβ superfamily growth factor signaling is mediated by diluting or removing an exogenously added TGFβ superfamily growth factor, such as activin A, from the cell culture or cell population of definitive endoderm. In other embodiments, TGFβ superfamily growth factor signaling is reduced or eliminated by providing the definitive endoderm cells with a compound that blocks TGFβ superfamily growth factor signaling, such as follistatin and/or noggin. In some embodiments, TGFβ superfamily growth factor signaling can be reduced or eliminated for about one day, about two days, about three days, about four days, about five days, about six days, about seven days, about eight days, about nine days, about ten days or greater than about ten days subsequent to the differentiation of the human pluripotent cells to definitive endoderm cells.

In some embodiments, differentiation of definitive endoderm cells to foregut endoderm cells is enhanced by providing the definitive endoderm cell culture or cell population with an FGF-family growth factor and/or a hedgehog pathway inhibitor. In such embodiments the FGF-family growth factor and/or hedgehog pathway inhibitor is provided at about one day, about two days, about three days, about four days, about five days, about six days, about seven days, about eight days, about nine days, about ten days or greater than about ten days subsequent to reducing or eliminating TGFβ superfamily growth factor signaling in the definitive endoderm cell culture. In a preferred embodiment, the FGF-family growth factor and/or hedgehog pathway inhibitor is provided at about the same time as reducing or eliminating TGFβ superfamily growth factor signaling in the definitive endoderm cell culture.

In a preferred embodiment, the FGF-family growth factor provided to the definitive endoderm cell culture or cell population is FGF10 and/or FGF7. However, it will be appreciated that other FGF-family growth factors or FGF-family growth factor analogs or mimetics may be provided instead of or in addition to FGF10 and/or FGF7. For example, an FGF-family growth factor selected from the group consisting of FGF1, FGF2, FGF3, FGF4, FGFS, FGF6, FGF7, FGF8, FGF9, FGF10, FGF11, FGF12, FGF13, FGF14, FGF15, FGF16, FGF17, FGF18, FGF19, FGF20, FGF21, FGF22 and/or FGF23 may be provided. In such embodiments, the FGF-family growth factor and/or the FGF-family growth factor analog or mimetic is provided to the cells of a cell culture such that it is present at a concentration of at least about 10 ng/ml, at least about 25 ng/ml, at least about 50 ng/ml, at least about 75 ng/ml, at least about 100 ng/ml, at least about 200 ng/ml, at least about 300 ng/ml, at least about 400 ng/ml, at least about 500 ng/ml, or at least about 1000 ng/ml.

In other preferred embodiments, the hedgehog inhibitor is KAAD-cyclopamine However, it will be appreciated that other hedgehog inhibitors can be used. Such inhibitors include, but are not limited to, KKAD-cyclopamine analogs, jervine, jervine analogs, hedgehog pathway blocking antibodies and any other inhibitors of hedgehog pathway function known to those of ordinary skill in the art. When used alone or in conjunction with FGF-family growth factor, the hedgehog inhibitor can be provided at a concentration of at least about 0.01 μM, at least about 0.02 μM, at least about 0.04 μM, at least about 0.08 μM, at least about 0.1 μM, at least about 0.2 μM, at least about 0.3 μM, at least about 0.4 μM, at least about 0.5 μM, at least about 0.6 μM, at least about 0.7 μM, at least about 0.8 μM, at least about 0.9 μM, at least about 1 μM, at least about 1.1 μM, at least about 1.2 μM, at least about 1.3 μM, at least about 1.4 μM, at least about 1.5 μM, at least about 1.6 μM, at least about 1.7 μM, at least about 1.8 μM, at least about 1.9 μM, at least about 2 μM, at least about 2.1 μM, at least about 2.2 μM, at least about 2.3 μM, at least about 2.4 μM, at least about 2.5 μM, at least about 2.6 μM, at least about 2.7 μM, at least about 2.8 μM, at least about 2.9 μM, at least about 3 μM, at least about 3.5 μM, at least about 4 μM, at least about 4.5 μM, at least about 5 μM, at least about 10 μM, at least about 20 μM, at least about 30 μM, at least about 40 μM or at least about 50 μM.

In a preferred process for the production of a population of PDX1-negative foregut endoderm cells from definitive endoderm cells, TGFβ superfamily growth factor signaling is reduced or eliminated for about two day subsequent to the differentiation of a substantial portion of human pluripotent cells to definitive endoderm (for example, after a three day, four or five day differentiation protocol as described in the examples below). At about the same time, the cell culture or cell population of definitive endoderm cells is provided with 50 ng/ml of FGF-10 and 0.2 μM KAAD-cyclopamine.

Cultures of PDX1-negative foregut endoderm cells can be differentiated and further grown in a medium containing reduced or no serum. Serum concentrations can range from about 0.05% (v/v) to about 20% (v/v). In some processes, PDX1-negative foregut endoderm cells are grown with serum replacement. For example, in certain processes, the serum concentration of the medium can be less than about 0.05% (v/v), less than about 0.1% (v/v), less than about 0.2% (v/v), less than about 0.3% (v/v), less than about 0.4% (v/v), less than about 0.5% (v/v), less than about 0.6% (v/v), less than about 0.7% (v/v), less than about 0.8% (v/v), less than about 0.9% (v/v), less than about 1% (v/v), less than about 2% (v/v), less than about 3% (v/v), less than about 4% (v/v), less than about 5% (v/v), less than about 6% (v/v), less than about 7% (v/v), less than about 8% (v/v), less than about 9% (v/v), less than about 10% (v/v), less than about 15% (v/v) or less than about 20% (v/v). In certain processes described herein, the differentiation medium does not include serum, serum replacement or any supplement comprising insulin or insulin-like growth factors.

In certain processes, PDX1-negative foregut endoderm cells are grown in the presence of B27. In such differentiation processes, B27 can be provided to the culture medium in concentrations ranging from about 0.1% (v/v) to about 20% (v/v) or in concentrations greater than about 20% (v/v). In certain processes, the concentration of B27 in the medium is about 0.1% (v/v), about 0.2% (v/v), about 0.3% (v/v), about 0.4% (v/v), about 0.5% (v/v), about 0.6% (v/v), about 0.7% (v/v), about 0.8% (v/v), about 0.9% (v/v), about 1% (v/v), about 2% (v/v), about 3% (v/v), about 4% (v/v), about 5% (v/v), about 6% (v/v), about 7% (v/v), about 8% (v/v), about 9% (v/v), about 10% (v/v), about 15% (v/v) or about 20% (v/v). Alternatively, the concentration of the added B27 supplement can be measured in terms of multiples of the strength of a commercially available B27 stock solution. For example, B27 is available from Invitrogen (Carlsbad, Calif.) as a 50X stock solution. Addition of a sufficient amount of this stock solution to a sufficient volume of growth medium produces a medium supplemented with the desired amount of B27. For example, the addition of 10 ml of 50X B27 stock solution to 90 ml of growth medium would produce a growth medium supplemented with 5X B27. The concentration of B27 supplement in the medium can be about 0.1X, about 0.2X, about 0.3X, about 0.4X, about 0.5X, about 0.6X, about 0.7X, about 0.8X, about 0.9X, about 1X, about 1.1X, about 1.2X, about 1.3X, about 1.4X, about 1.5X, about 1.6X, about 1.7X, about 1.8X, about 1.9X, about 2X, about 2.5X, about 3X, about 3.5X, about 4X, about 4.5X, about 5X, about 6X, about 7X, about 8X, about 9X, about 10X, about 11X, about 12X, about 13X, about 14X, about 15X, about 16X, about 17X, about 18X, about 19X, about 20X and greater than about 20X.

In some embodiments, the PDX1-negative foregut endoderm cells can be further differentiated to PDX1-positive foregut endoderm cells by contacting the cells with a medium comprising, or otherwise providing to the cells, a retinoid, such as retinoic acid (RA).

In some embodiments, the retinoid is provided to the cells of a cell culture such that it is present at a concentration of at least about 1 nM, at least about 0.01 μM, at least about 0.02 μM, at least about 0.04 μM, at least about 0.08 μM, at least about 0.1 μM, at least about 0.2 μM, at least about 0.3 μM, at least about 0.4 μM, at least about 0.5 μM, at least about 0.6 μM, at least about 0.7 μM, at least about 0.8 μM, at least about 0.9 μM, at least about 1 μM, at least about 1.1 μM, at least about 1.2 μM, at least about 1.3 μM, at least about 1.4 μM, at least about 1.5 μM, at least about 1.6 μM, at least about 1.7 μM, at least about 1.8 μM, at least about 1.9 μM, at least about 2 μM, at least about 2.1 μM, at least about 2.2 μM, at least about 2.3 μM, at least about 2.4 μM, at least about 2.5 μM, at least about 2.6 μM, at least about 2.7 μM, at least about 2.8 μM, at least about 2.9 μM, at least about 3 μM, at least about 3.5 μM, at least about 4 μM, at least about 4.5 μM, at least about 5 μM, at least about 10 μM, at least about 20 μM, at least about 30 μM, at least about 40 μM or at least about 50 μM. In such embodiments, the retinoid is provided to the cells at about one day, about two days, about three days, about four days, about five days, about six days, about seven days, about eight days, about nine days, about ten days or greater than about ten days subsequent to reducing or eliminating TGFβ superfamily growth factor signaling in the definitive endoderm cell culture. In a preferred embodiment, from about 0.05 μM RA to about 2 μM RA is provided to the PDX-1 negative foregut endoderm cell culture about 2 to 3 days subsequent to reducing or eliminating TGFβ superfamily growth factor signaling.

In some of the differentiation processes described herein, the above-mentioned differentiation factors are removed from the cell culture subsequent to their addition. For example, the above-mentioned differentiation factors can be removed within about one day, about two days, about three days, about four days, about five days, about six days, about seven days, about eight days, about nine days or about ten days after their addition.

Monitoring the Differentiation of PDX1-Negative Definitive Endoderm to PDX1-Negative Foregut Endoderm

Expression of HNF1b and/or FOXA1 and the lack of expression of PDX1 can be detected and/or quantitated using the above-described methods, such as Q-PCR and/or immunocytochemistry, to monitor the differentiation of PDX1-negative definitive endoderm to PDX1-negative foregut endoderm. In addition to the above-described markers, in some embodiments of the present invention, the expression of SOX17 is also determined.

In some embodiments, PDX1-negative foregut endoderm cell cultures produced by the methods described herein are substantially free of cells expressing the SOX7, AFP, SOX1, ZIC1 or NFM marker genes. In certain embodiments, the PDX1-negative foregut endoderm cell cultures produced by the processes described herein are substantially free of visceral endoderm, parietal endoderm and/or neural cells.

Compositions Comprising PDX1-Negative Foregut Endoderm

Some embodiments of the present invention relate to cell compositions, such as cell cultures or cell populations, comprising PDX1-negative foregut endoderm cells, wherein the PDX1-negtive foregut endoderm cells are multipotent cells that can differentiate into cells, tissues or organs derived from the anterior portion of the gut tube. In accordance with certain embodiments, the PDX1-negative foregut endoderm cells are mammalian cells, and in a preferred embodiment, such cells are human cells.

Other embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising cells of one or more cell types selected from the group consisting of hESCs, PDX1-negative definitive endoderm cells, PDX1-negative foregut endoderm cells and mesoderm cells. In some embodiments, hESCs comprise less than about 5%, less than about 4%, less than about 3%, less than about 2% or less than about 1% of the total cells in the culture. In other embodiments, PDX1-negative definitive endoderm cells comprise less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 12%, less than about 10%, less than about 8%, less than about 6%, less than about 5%, less than about 4%, less than about 3%, less than about 2% or less than about 1% of the total cells in the culture. In yet other embodiments, mesoderm cells comprise less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 12%, less than about 10%, less than about 8%, less than about 6%, less than about 5%, less than about 4%, less than about 3%, less than about 2% or less than about 1% of the total cells in the culture.

Additional embodiments of the present invention relate to compositions, such as cell cultures or cell populations, produced by the processes described herein comprise PDX1-negative foregut endoderm as the majority cell type. In some embodiments, the processes described herein produce cell cultures and/or cell populations comprising at least about 99%, at least about 98%, at least about 97%, at least about 96%, at least about 95%, at least about 94%, at least about 93%, at least about 92%, at least about 91%, at least about 90%, at least about 89%, at least about 88%, at least about 87%, at least about 86%, at least about 85%, at least about 84%, at least about 83%, at least about 82%, at least about 81%, at least about 80%, at least about 79%, at least about 78%, at least about 77%, at least about 76%, at least about 75%, at least about 74%, at least about 73%, at least about 72%, at least about 71%, at least about 70%, at least about 69%, at least about 68%, at least about 67%, at least about 66%, at least about 65%, at least about 64%, at least about 63%, at least about 62%, at least about 61%, at least about 60%, at least about 59%, at least about 58%, at least about 57%, at least about 56%, at least about 55%, at least about 54%, at least about 53%, at least about 52%, at least about 51% or at least about 50% PDX1-negative foregut endoderm cells. In preferred embodiments the cells of the cell cultures or cell populations comprise human cells. In other embodiments, the processes described herein produce cell cultures or cell populations comprising at least about 50%, at least about 45%, at least about 40%, at least about 35%, at least about 30%, at least about 25%, at least about 24%, at least about 23%, at least about 22%, at least about 21%, at least about 20%, at least about 19%, at least about 18%, at least about 17%, at least about 16%, at least about 15%, at least about 14%, at least about 13%, at least about 12%, at least about 11%, at least about 10%, at least about 9%, at least about 8%, at least about 7%, at least about 6%, at least about 5%, at least about 4%, at least about 3%, at least about 2% or at least about 1% PDX1-negative foregut endoderm cells. In preferred embodiments, the cells of the cell cultures or cell populations comprise human cells. In some embodiments, the percentage of PDX1-negative foregut endoderm cells in the cell cultures or populations is calculated without regard to the feeder cells remaining in the culture.

Still other embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising PDX1-negative foregut endoderm cells and PDX1-negative definitive endoderm cells. For example, cell cultures or cell populations comprising at least about 5 PDX1-negative foregut endoderm cells for about every 95 PDX1-negative definitive endoderm cells can be produced. In other embodiments, cell cultures or cell populations comprising at least about 95 PDX1-negative foregut endoderm cells for about every 5 PDX1-negative definitive endoderm cells can be produced. Additionally, cell cultures or cell populations comprising other ratios of PDX1-negative foregut endoderm cells to PDX1-negative definitive endoderm cells are contemplated. For example, compositions comprising at least about 1 PDX1-negative foregut endoderm cell for about every 1,000,000 PDX1-negative definitive endoderm cells, at least about 1 PDX1-negative foregut endoderm cell for about every 100,000 PDX1-negative definitive endoderm cells, at least about 1 PDX1-negative foregut endoderm cell for about every 10,000 PDX1-negative definitive endoderm cells, at least about 1 PDX1-negative foregut endoderm cell for about every 1000 PDX1-negative definitive endoderm cells, at least about 1 PDX1-negative foregut endoderm cell for about every 500 PDX1-negative definitive endoderm cells, at least about 1 PDX1-negative foregut endoderm cell for about every 100 PDX1-negative definitive endoderm cells, at least about 1 PDX1-negative foregut endoderm cell for about every 10 PDX1-negative definitive endoderm cells, at least about 1 PDX1-negative foregut endoderm cell for about every 5 PDX1-negative definitive endoderm cells, at least about 1 PDX1-negative foregut endoderm cell for about every 4 PDX1-negative definitive endoderm cells, at least about 1 PDX1-negative foregut endoderm cell for about every 2 PDX1-negative definitive endoderm cells, at least about 1 PDX1-negative foregut endoderm cell for about every 1 PDX1-negative definitive endoderm cell, at least about 2 PDX1-negative foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 4 PDX1-negative foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 5 PDX1-negative foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 10 PDX1-negative foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 20 PDX1-negative foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 50 PDX1-negative foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 100 PDX1-negative foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 1000 PDX1-negative foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 10,000 PDX1-negative foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 100,000 PDX1-negative foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell and at least about 1,000,000 PDX1-negative foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell are contemplated.

In some embodiments of the present invention, the PDX1-negative definitive endoderm cells from which PDX1-negative foregut endoderm cells are produced are derived from human pluripotent cells, such as human pluripotent stem cells. In certain embodiments, the human pluripotent cells are derived from a morula, the inner cell mass of an embryo or the gonadal ridges of an embryo. In certain other embodiments, the human pluripotent cells are derived from the gonadal or germ tissues of a multicellular structure that has developed past the embryonic stage.

Further embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising human cells, including human PDX1-negative foregut endoderm cells, wherein the expression of the SOX17, HNF1b and/or FOXA1 marker is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 2% of the human cells. In other embodiments, the expression of the SOX17, HNF1b and/or FOXA1 marker is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 5% of the human cells, in at least about 10% of the human cells, in at least about 15% of the human cells, in at least about 20% of the human cells, in at least about 25% of the human cells, in at least about 30% of the human cells, in at least about 35% of the human cells, in at least about 40% of the human cells, in at least about 45% of the human cells, in at least about 50% of the human cells, in at least about 55% of the human cells, in at least about 60% of the human cells, in at least about 65% of the human cells, in at least about 70% of the human cells, in at least about 75% of the human cells, in at least about 80% of the human cells, in at least about 85% of the human cells, in at least about 90% of the human cells, in at least about 95% of the human cells or in at least about 98% of the human cells. In some embodiments, the percentage of human cells in the cell cultures or populations, wherein the expression of SOX17, HNF1b and/or FOXA1 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker, is calculated without regard to feeder cells.

It will be appreciated that some embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising human PDX1-negative foregut endoderm cells, wherein the expression of one or more markers selected from the group consisting of SOX17, HNF1b and/or FOXA1 is greater than the expression of the PDX1 marker in from at least about 2% to greater than at least about 98% of the human cells. In some embodiments, the expression of one or more markers selected from the group consisting of SOX17, HNF1b and/or FOXA1 is greater than the expression of the PDX1 marker in at least about 5% of the human cells, in at least about 10% of the human cells, in at least about 15% of the human cells, in at least about 20% of the human cells, in at least about 25% of the human cells, in at least about 30% of the human cells, in at least about 35% of the human cells, in at least about 40% of the human cells, in at least about 45% of the human cells, in at least about 50% of the human cells, in at least about 55% of the human cells, in at least about 60% of the human cells, in at least about 65% of the human cells, in at least about 70% of the human cells, in at least about 75% of the human cells, in at least about 80% of the human cells, in at least about 85% of the human cells, in at least about 90% of the human cells, in at least about 95% of the human cells or in at least about 98% of the human cells. In some embodiments, the percentage of human cells in the cell cultures or populations, wherein the expression of one or more markers selected from the group consisting of SOX17, HNF1b and/or FOXA1 is greater than the expression of the PDX1 marker, is calculated without regard to feeder cells.

Using the processes described herein, compositions comprising PDX1-negative foregut endoderm cells substantially free of other cell types can be produced. With respect to cells in cell cultures or in cell populations, the term “substantially free of” means that the specified cell type of which the cell culture or cell population is free, is present in an amount of less than about 5% of the total number of cells present in the cell culture or cell population. In some embodiments of the present invention, the PDX1-negative foregut endoderm cell populations or cell cultures produced by the methods described herein are substantially free of cells that significantly express the AFP, SOX7, SOX1, ZIC1 and/or NFM marker genes.

In one embodiment of the present invention, a description of a PDX1-negative foregut endoderm cell based on the expression of marker genes is, SOX17 high, HNF1b high, FOXA1 high, PDX1 low, AFP low, SOX7 low, SOX1 low, ZIC1 low and NFM low.

Production of PDX1-Positve Foregut Endoderm Directly from PDX1-Negative Definitive Endoderm

The PDX1-positive foregut endoderm cell cultures and populations comprising PDX1-positive foregut endoderm cells that are described herein are produced from PDX1-negative definitive endoderm, which is generated from pluripotent cells as described above. A preferred method utilizes human embryonic stem cells as the starting material. In one embodiment, hESCs are first converted to PDX1-negative definitive endoderm cells, which are then converted to PDX1-positive foregut endoderm cells. It will be appreciated, however, that the starting materials for the production of PDX1-positive foregut endoderm is not limited to definitive endoderm cells produced using pluripotent cell differentiation methods. Rather, any PDX1-negative definitive endoderm cells can be used in the methods described herein regardless of their origin.

In some embodiments of the present invention, cell cultures or cell populations comprising PDX1-negative definitive endoderm cells can be used for further differentiation to cell cultures and/or enriched cell populations comprising PDX1-positive foregut endoderm cells. For example, a cell culture or cell population comprising human PDX1-negative, SOX17-positive definitive endoderm cells can be used. In some embodiments, the cell culture or cell population may also comprise differentiation factors, such as activins, nodals and/or BMPs, remaining from the previous differentiation step (that is, the step of differentiating pluripotent cells to definitive endoderm cells). In other embodiments, factors utilized in the previous differentiation step are removed from the cell culture or cell population prior to the addition of factors used for the differentiation of the PDX1-negative, SOX17-positive definitive endoderm cells to PDX1-positive foregut endoderm cells. In other embodiments, cell populations enriched for PDX1-negative, SOX17-positive definitive endoderm cells are used as a source for the production of PDX1-positive foregut endoderm cells.

PDX1-negative definitive endoderm cells in culture are differentiated to PDX1-positive endoderm cells by providing to a cell culture comprising PDX1-negative, SOX17-positive definitive endoderm cells a differentiation factor that promotes differentiation of the cells to PDX1-positive foregut endoderm cells (foregut differentiation factor). In some embodiments of the present invention, the foregut differentiation factor is retinoid, such as retinoic acid (RA). In some embodiments, the retinoid is used in conjunction with a fibroblast growth factor, such as FGF-4 or FGF-10. In other embodiments, the retinoid is used in conjunction with a member of the TGFβ superfamily of growth factors and/or a conditioned medium.

By “conditioned medium” is meant, a medium that is altered as compared to a base medium. For example, the conditioning of a medium may cause molecules, such as nutrients and/or growth factors, to be added to or depleted from the original levels found in the base medium. In some embodiments, a medium is conditioned by allowing cells of certain types to be grown or maintained in the medium under certain conditions for a certain period of time. For example, a medium can be conditioned by allowing hESCs to be expanded, differentiated or maintained in a medium of defined composition at a defined temperature for a defined number of hours. As will be appreciated by those of skill in the art, numerous combinations of cells, media types, durations and environmental conditions can be used to produce nearly an infinite array of conditioned media. In some embodiments of the present invention, a medium is conditioned by allowing differentiated pluripotent cells to be grown or maintained in a medium comprising about 1% to about 20% serum concentration. In other embodiments, a medium is conditioned by allowing differentiated pluripotent cells to be grown or maintained in a medium comprising about 1 ng/ml to about 1000 ng/ml activin A. In still other embodiments, a medium is conditioned allowing differentiated pluripotent cells to be grown or maintained in a medium comprising about 1 ng/ml to about 1000 ng/ml BMP4. In a preferred embodiment, a conditioned medium is prepared by allowing differentiated hESCs to be grown or maintained for 24 hours in a medium, such as RPMI, comprising about 25 ng/ml activin A and about 2 μM RA.

In some embodiments of the present invention, the cells used to condition the medium, which is used to enhance the differentiation of PDX1-negative definitive endoderm to PDX1-positive foregut endoderm, are cells that are differentiated from pluripotent cells, such as hESCs, over about a 5 day time period in a medium such as RPMI comprising about 0% to about 20% serum and/or one or more growth/differentiation factors of the TGFβ superfamily. Differentiation factors, such as activin A and BMP4 are supplied at concentrations ranging from about 1 ng/ml to about 1000 ng/ml. In certain embodiments of the present invention, the cells used to condition the medium are differentiated from hESCs over about a 5 day period in low serum RPMI. According to some embodiments, low serum RPMI refers to a low serum containing medium, wherein the serum concentration is gradually increased over a defined time period. For example, in one embodiment, low serum RPMI comprises a concentration of about 0.2% fetal bovine serum (FBS) on the first day of cell growth, about 0.5% FBS on the second day of cell growth and about 2% FBS on the third through fifth day of cell growth. In another embodiment, low serum RPMI comprises a concentration of about 0% on day one, about 0.2% on day two and about 2% on days 3-6. In certain preferred embodiments, low serum RPMI is supplemented with one or more differentiation factors, such as activin A and BMP4. In addition to its use in preparing cells used to condition media, low serum RPMI can be used as a medium for the differentiation of PDX1-positive foregut endoderm cells from PDX1-negative definitive endoderm cells.

It will be appreciated by those of ordinary skill in the art that conditioned media can be prepared from media other than RPMI provided that such media do not interfere with the growth or maintenance of PDX1-positive foregut endoderm cells. It will also be appreciated that the cells used to condition the medium can be of various types. In embodiments where freshly differentiated cells are used to condition a medium, such cells can be differentiated in a medium other than RPMI provided that the medium does not inhibit the growth or maintenance of such cells. Furthermore, a skilled artisan will appreciate that neither the duration of conditioning nor the duration of preparation of cells used for conditioning is required to be 24 hours or 5 days, respectively, as other time periods will be sufficient to achieve the effects reported herein.

In general, the use of a retinoid in combination with a fibroblast growth factor, a member of the TGFβ superfamily of growth factors, a conditioned medium or a combination of any of these foregut differentiation factors causes greater differentiation of PDX1-negative definitive endoderm to PDX1-positive foregut endoderm than the use of a retinoid alone. In a preferred embodiment, RA and FGF-10 are both provided to the PDX1-negative definitive endoderm cell culture. In another preferred embodiment, PDX1-negative definitive endoderm cells are differentiated in a culture comprising a conditioned medium, activin A, activin B and RA.

With respect to some of the embodiments of differentiation processes described herein, the above-mentioned foregut differentiation factors are provided to the cells so that these factors are present in the cell culture or cell population at concentrations sufficient to promote differentiation of at least a portion of the PDX1-negative definitive endoderm cell culture or cell population to PDX1-positive foregut endoderm cells. When used in connection with cell cultures and/or cell populations, the term “portion” means any non-zero amount of the cell culture or cell population, which ranges from a single cell to the entirety of the cell culture or cells population.

In some embodiments of the present invention, a retinoid is provided to the cells of a cell culture such that it is present at a concentration of at least about 0.01 μM, at least about 0.02 μM, at least about 0.04 μM, at least about 0.08 μM, at least about 0.1 μM, at least about 0.2 μM, at least about 0.3 μM, at least about 0.4 μM, at least about 0.5 μM, at least about 0.6 μM, at least about 0.7 μM, at least about 0.8 μM, at least about 0.9 μM, at least about 1 μM, at least about 1.1 μM, at least about 1.2 μM, at least about 1.3 μM, at least about 1.4 μM, at least about 1.5 μM, at least about 1.6 μM, at least about 1.7 μM, at least about 1.8 μM, at least about 1.9 μM, at least about 2 μM, at least about 2.1 μM, at least about 2.2 μM, at least about 2.3 μM, at least about 2.4 μM, at least about 2.5 μM, at least about 2.6 μM, at least about 2.7 μM, at least about 2.8 μM, at least about 2.9 μM, at least about 3 μM, at least about 3.5 μM, at least about 4 μM, at least about 4.5 μM, at least about 5 μM, at least about 10 μM, at least about 20 μM, at least about 30 μM, at least about 40 μM or at least about 50 μM. As used herein, “retinoid” refers to retinol, retinal or retinoic acid as well as derivatives of any of these compounds. In a preferred embodiment, the retinoid is retinoic acid.

In other embodiments of the present invention, one or more differentiation factors of the fibroblast growth factor family are present in the cell culture. For example, in some embodiments, FGF-4 can be present in the cell culture at a concentration of at least about 10 ng/ml, at least about 25 ng/ml, at least about 50 ng/ml, at least about 75 ng/ml, at least about 100 ng/ml, at least about 200 ng/ml, at least about 300 ng/ml, at least about 400 ng/ml, at least about 500 ng/ml, or at least about 1000 ng/ml. In further embodiments of the present invention, FGF-10 is present in the cell culture at a concentration of at least about 10 ng/ml, at least about 25 ng/ml, at least about 50 ng/ml, at least about 75 ng/ml, at least about 100 ng/ml, at least about 200 ng/ml, at least about 300 ng/ml, at least about 400 ng/ml, at least about 500 ng/ml, or at least about 1000 ng/ml. In some embodiments, either FGF-4 or FGF-10, but not both, is provided to the cell culture along with RA. In a preferred embodiment, RA is present in the cell culture at 1 μM and FGF-10 is present at a concentration of 50 ng/ml.

In some embodiments of the present invention, growth factors of the TGFβ superfamily and/or a conditioned medium are present in the cell culture. These differentiation factors can be used in combination with RA and/or other mid-foregut differentiation factors including, but not limited to, FGF-4 and FGF-10. For example, in some embodiments, activin A and/or activin B can be present in the cell culture at a concentration of at least about 5 ng/ml, at least about 10 ng/ml, at least about 25 ng/ml, at least about 50 ng/ml, at least about 75 ng/ml, at least about 100 ng/ml, at least about 200 ng/ml, at least about 300 ng/ml, at least about 400 ng/ml, at least about 500 ng/ml, or at least about 1000 ng/ml. In further embodiments of the present invention, a conditioned medium is present in the cell culture at a concentration of at least about 1%, at least about 5%, at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 100% of the total medium. In some embodiments, activin A, activin B and a conditioned medium are provided to the cell culture along with RA. In a preferred embodiment, PDX1-negative definitive endoderm cells are differentiated to PDX1-positive foregut endoderm cells in cultures comprising about 1 μM RA, about 25 ng/ml activin A and low serum RPMI medium that has been conditioned for about 24 hours by differentiated hESCs, wherein the differentiated hESCs have been differentiated for about 5 days in low serum RPMI comprising about 100 ng/ml activin A. In another preferred embodiment, activin B and/or FGF-10 are also present in the culture at 25 ng/ml and 50 ng/ml, respectively.

In certain embodiments of the present invention, the above-mentioned foregut differentiation factors are removed from the cell culture subsequent to their addition. For example, the foregut differentiation factors can be removed within about one day, about two days, about three days, about four days, about five days, about six days, about seven days, about eight days, about nine days or about ten days after their addition.

Cultures of PDX1-positive foregut endoderm cells can be grown in a medium containing reduced serum. Serum concentrations can range from about 0.05% (v/v) to about 20% (v/v). In some embodiments, PDX1-positive foregut endoderm cells are grown with serum replacement. For example, in certain embodiments, the serum concentration of the medium can be less than about 0.05% (v/v), less than about 0.1% (v/v), less than about 0.2% (v/v), less than about 0.3% (v/v), less than about 0.4% (v/v), less than about 0.5% (v/v), less than about 0.6% (v/v), less than about 0.7% (v/v), less than about 0.8% (v/v), less than about 0.9% (v/v), less than about 1% (v/v), less than about 2% (v/v), less than about 3% (v/v), less than about 4% (v/v), less than about 5% (v/v), less than about 6% (v/v), less than about 7% (v/v), less than about 8% (v/v), less than about 9% (v/v), less than about 10% (v/v), less than about 15% (v/v) or less than about 20% (v/v). In some embodiments, PDX1-positive foregut endoderm cells are grown without serum. In other embodiments, PDX1-positive foregut endoderm cells are grown with serum replacement.

In still other embodiments, PDX1-positive foregut endoderm cells are grown in the presence of B27. In such embodiments, B27 can be provided to the culture medium in concentrations ranging from about 0.1% (v/v) to about 20% (v/v) or in concentrations greater than about 20% (v/v). In certain embodiments, the concentration of B27 in the medium is about 0.1% (v/v), about 0.2% (v/v), about 0.3% (v/v), about 0.4% (v/v), about 0.5% (v/v), about 0.6% (v/v), about 0.7% (v/v), about 0.8% (v/v), about 0.9% (v/v), about 1% (v/v), about 2% (v/v), about 3% (v/v), about 4% (v/v), about 5% (v/v), about 6% (v/v), about 7% (v/v), about 8% (v/v), about 9% (v/v), about 10% (v/v), about 15% (v/v) or about 20% (v/v). Alternatively, the concentration of the added B27 supplement can be measured in terms of multiples of the strength of a commercially available B27 stock solution. For example, B27 is available from Invitrogen (Carlsbad, Calif.) as a 50X stock solution. Addition of a sufficient amount of this stock solution to a sufficient volume of growth medium produces a medium supplemented with the desired amount of B27. For example, the addition of 10 ml of 50X B27 stock solution to 90 ml of growth medium would produce a growth medium supplemented with 5X B27. The concentration of B27 supplement in the medium can be about 0.1X, about 0.2X, about 0.3X, about 0.4X, about 0.5X, about 0.6X, about 0.7X, about 0.8X, about 0.9X, about 1X, about 1.1X, about 1.2X, about 1.3X, about 1.4X, about 1.5X, about 1.6X, about 1.7X, about 1.8X, about 1.9X, about 2X, about 2.5X, about 3X, about 3.5X, about 4X, about 4.5X, about 5X, about 6X, about 7X, about 8X, about 9X, about 10X, about 11X, about 12X, about 13X, about 14X, about 15X, about 16X, about 17X, about 18X, about 19X, about 20X and greater than about 20X.

Production of Dorsal PDX1-Positve Foregut Endoderm from PDX1-Negative Definitive Endoderm

The dorsal PDX1-positive foregut endoderm cell cultures and populations comprising dorsal PDX1-positive foregut endoderm cells that are described herein are produced from PDX1-negative definitive endoderm, which is generated from pluripotent cells as described above. Furthermore, as described above, a preferred method utilizes human embryonic stem cells as the starting material. In one embodiment, hESCs are first converted to PDX1-negative definitive endoderm cells, which are then converted to dorsal PDX1-positive foregut endoderm cells. It will be appreciated, however, that the starting materials for the production of dorsal PDX1-positive foregut endoderm is not limited to definitive endoderm cells produced using pluripotent cell differentiation methods. Rather, any PDX1-negative definitive endoderm cells can be used in the methods described herein regardless of their origin.

As described in connection with the production of mixed populations of PDX1-positive foregut endoderm cells, in some embodiments of the present invention, cell cultures or cell populations comprising PDX1-negative definitive endoderm cells can be used for further differentiation to cell cultures and/or enriched cell populations comprising dorsal PDX1-positive foregut endoderm cells. For example, a cell culture or cell population comprising human PDX1-negative, SOX17-positive definitive endoderm cells can be used. In some embodiments, the cell culture or cell population may also comprise differentiation factors, such as activins, nodals and/or BMPs, remaining from the previous differentiation step (that is, the step of differentiating pluripotent cells to definitive endoderm cells). In other embodiments, factors utilized in the previous differentiation step are removed from the cell culture or cell population prior to the addition of factors used for the differentiation of the PDX1-negative, SOX17-positive definitive endoderm cells to dorsal PDX1-positive foregut endoderm cells. In other embodiments, cell populations enriched for PDX1-negative, SOX17-positive definitive endoderm cells are used as a source for the production of dorsal PDX1-positive foregut endoderm cells.

PDX1-negative definitive endoderm cells in culture are differentiated to dorsal PDX1-positive endoderm cells by providing to a cell culture comprising PDX1-negative, SOX17-positive definitive endoderm cells a retinoid, such as retinoic acid (RA). In some embodiments, the retinoid is used in conjunction with a member of the TGFβ superfamily of growth factors and/or Connaught Medical Research Labs medium (CRML medium) (Invitrogen, Carlsbad, Calif.).

With respect to some of the embodiments of differentiation processes described herein, the RA or a combination of the above-mentioned differentiation factors are provided to the cells so that these factors are present in the cell culture or cell population at concentrations sufficient to promote differentiation of at least a portion of the PDX1-negative definitive endoderm cell culture or cell population to dorsal PDX1-positive foregut endoderm cells. When used in connection with cell cultures and/or cell populations, the term “portion” means any non-zero amount of the cell culture or cell population, which ranges from a single cell to the entirety of the cell culture or cell population. In preferred embodiments, the term “portion” means at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 11%, at least 12%, at least 13%, at least 14%, at least 15%, at least 16%, at least 17%, at least 18%, at least 19%, at least 20%, at least 21%, at least 22%, at least 23%, at least 24%, at least 25%, at least 26%, at least 27%, at least 28%, at least 29%, at least 30%, at least 31%, at least 32%, at least 33%, at least 34%, at least 35%, at least 36%, at least 37%, at least 38%, at least 39%, at least 40%, at least 41%, at least 42%, at least 43%, at least 44%, at least 45%, at least 46%, at least 47%, at least 48%, at least 49%, at least 50%, at least 51%, at least 52%, at least 53%, at least 54%, at least 55%, at least 56%, at least 57%, at least 58%, at least 59%, at least 60%, at least 61%, at least 62%, at least 63%, at least 64%, at least 65%, at least 66%, at least 67%, at least 68%, at least 69%, at least 70%, at least 71%, at least 72%, at least 73%, at least 74% or at least 75% of the cell culture or cell population.

In some embodiments of the present invention, a retinoid is provided to the cells of a cell culture such that it is present at a concentration of at least about 0.01 μM, at least about 0.02 μM, at least about 0.04 μM, at least about 0.08 μM, at least about 0.1 μM, at least about 0.2 μM, at least about 0.3 μM, at least about 0.4 μM, at least about 0.5 μM, at least about 0.6 μM, at least about 0.7 μM, at least about 0.8 μM, at least about 0.9 μM, at least about 1 μM, at least about 1.1 μM, at least about 1.2 μM, at least about 1.3 μM, at least about 1.4 μM, at least about 1.5 μM, at least about 1.6 μM, at least about 1.7 μM, at least about 1.8 μM, at least about 1.9 μM, at least about 2 μM, at least about 2.1 μM, at least about 2.2 μM, at least about 2.3 μM, at least about 2.4 μM, at least about 2.5 μM, at least about 2.6 μM, at least about 2.7 μM, at least about 2.8 μM, at least about 2.9 μM, at least about 3 μM, at least about 3.5 μM, at least about 4 μM, at least about 4.5 μM, at least about 5 μM, at least about 10 μM, at least about 20 μM, at least about 30 μM, at least about 40 μM or at least about 50 μM.

In preferred embodiments of the present invention, a population of dorsally-biased PDX1-positive foregut endoderm cells is produced by providing retinoic acid in the absence of exogenous FGF-10 or other FGF family growth factor. In such embodiments, RA is provided at a concentration of about 2 μM. In a preferred embodiment, RA is provided at a concentration of about 2 μM in CMRL medium.

In some embodiments, activin A and/or activin B are provided to the cell culture along with RA. For example, in some embodiments, RA is provided to the cell culture at a concentration of about 2 μM and activin A and/or activin B is provided to the cell culture at a concentration of at least about 5 ng/ml, at least about 10 ng/ml, at least about 25 ng/ml, at least about 50 ng/ml, at least about 75 ng/ml, at least about 100 ng/ml, at least about 200 ng/ml, at least about 300 ng/ml, at least about 400 ng/ml, at least about 500 ng/ml, or at least about 1000 ng/ml.

In some embodiments, the differentiation factors and/or CRML medium is provided to the PDX1-negative definitive endoderm cells at about three days, at about four days, at about five days, at about six days, at about seven days, at about eight days, at about nine days, at about ten days or at about greater than ten days subsequent to the initiation of differentiation from hESCs. In preferred embodiments, differentiation factors and/or CRML medium is provided to the PDX1-negative definitive endoderm cells at about five days subsequent to the initiation of differentiation from hESCs.

In certain embodiments of the present invention, the above-mentioned differentiation factors are removed from the cell culture subsequent to their addition. For example, the above-mentioned differentiation factors can be removed within about one day, about two days, about three days, about four days, about five days, about six days, about seven days, about eight days, about nine days or about ten days after their addition.

Cultures of dorsal PDX1-positive foregut endoderm cells can be grown in a medium containing reduced serum. Serum concentrations can range from about 0.05% (v/v) to about 20% (v/v). In some embodiments, dorsal PDX1-positive foregut endoderm cells are grown with serum replacement. For example, in certain embodiments, the serum concentration of the medium can be less than about 0.05% (v/v), less than about 0.1% (v/v), less than about 0.2% (v/v), less than about 0.3% (v/v), less than about 0.4% (v/v), less than about 0.5% (v/v), less than about 0.6% (v/v), less than about 0.7% (v/v), less than about 0.8% (v/v), less than about 0.9% (v/v), less than about 1% (v/v), less than about 2% (v/v), less than about 3% (v/v), less than about 4% (v/v), less than about 5% (v/v), less than about 6% (v/v), less than about 7% (v/v), less than about 8% (v/v), less than about 9% (v/v), less than about 10% (v/v), less than about 15% (v/v) or less than about 20% (v/v). In some embodiments, dorsal PDX1-positive foregut endoderm cells are grown without serum. In other embodiments, dorsal PDX1-positive foregut endoderm cells are grown with serum replacement.

In still other embodiments, dorsal PDX1-positive foregut endoderm cells are grown in the presence of B27. In such embodiments, B27 can be provided to the culture medium in concentrations ranging from about 0.1% (v/v) to about 20% (v/v) or in concentrations greater than about 20% (v/v). In certain embodiments, the concentration of B27 in the medium is about 0.1% (v/v), about 0.2% (v/v), about 0.3% (v/v), about 0.4% (v/v), about 0.5% (v/v), about 0.6% (v/v), about 0.7% (v/v), about 0.8% (v/v), about 0.9% (v/v), about 1% (v/v), about 2% (v/v), about 3% (v/v), about 4% (v/v), about 5% (v/v), about 6% (v/v), about 7% (v/v), about 8% (v/v), about 9% (v/v), about 10% (v/v), about 15% (v/v) or about 20% (v/v). Alternatively, the concentration of the added B27 supplement can be measured in terms of multiples of the strength of a commercially available B27 stock solution. For example, B27 is available from Invitrogen (Carlsbad, Calif.) as a 50X stock solution. Addition of a sufficient amount of this stock solution to a sufficient volume of growth medium produces a medium supplemented with the desired amount of B27. For example, the addition of 10 ml of 50X B27 stock solution to 90 ml of growth medium would produce a growth medium supplemented with 5X B27. The concentration of B27 supplement in the medium can be about 0.1X, about 0.2X, about 0.3X, about 0.4X, about 0.5X, about 0.6X, about 0.7X, about 0.8X, about 0.9X, about 1X, about 1.1X, about 1.2X, about 1.3X, about 1.4X, about 1.5X, about 1.6X, about 1.7X, about 1.8X, about 1.9X, about 2X, about 2.5X, about 3X, about 3.5X, about 4X, about 4.5X, about 5X, about 6X, about 7X, about 8X, about 9X, about 10X, about 11X, about 12X, about 13X, about 14X, about 15X, about 16X, about 17X, about 18X, about 19X, about 20X and greater than about 20X.

Production of Ventral PDX1-Positve Foregut Endoderm from PDX1-Negative Definitive Endoderm

The ventral PDX1-positive foregut endoderm cell cultures and populations comprising ventral PDX1-positive foregut endoderm cells that are described herein are produced from PDX1-negative definitive endoderm, which is generated from pluripotent cells as described above. Furthermore, as described above, a preferred method utilizes human embryonic stem cells as the starting material. In one embodiment, hESCs are first converted to PDX1-negative definitive endoderm cells, which are then converted to ventral PDX1-positive foregut endoderm cells. It will be appreciated, however, that the starting materials for the production of ventral PDX1-positive foregut endoderm is not limited to definitive endoderm cells produced using pluripotent cell differentiation methods. Rather, any PDX1-negative definitive endoderm cells can be used in the methods described herein regardless of their origin.

As described in connection with the production of mixed populations of PDX1-positive foregut endoderm cells, in some embodiments of the present invention, cell cultures or cell populations comprising PDX1-negative definitive endoderm cells can be used for further differentiation to cell cultures and/or enriched cell populations comprising ventral PDX1-positive foregut endoderm cells. For example, a cell culture or cell population comprising human PDX1-negative, SOX17-positive definitive endoderm cells can be used. In some embodiments, the cell culture or cell population may also comprise differentiation factors, such as activins, nodals and/or BMPs, remaining from the previous differentiation step (that is, the step of differentiating pluripotent cells to definitive endoderm cells). In other embodiments, factors utilized in the previous differentiation step are removed from the cell culture or cell population prior to the addition of factors used for the differentiation of the PDX1-negative, SOX17-positive definitive endoderm cells to ventral PDX1-positive foregut endoderm cells. In other embodiments, cell populations enriched for PDX1-negative, SOX17-positive definitive endoderm cells are used as a source for the production of ventral PDX1-positive foregut endoderm cells.

PDX1-negative definitive endoderm cells in culture are differentiated to ventral PDX1-positive endoderm cells by providing to a cell culture comprising PDX1-negative, SOX17-positive definitive endoderm cells an FGF-family growth factor or FGF-family growth factor analog or mimetic. In some embodiments, the FGF-family growth factor or FGF-family growth factor analog or mimetic is used in conjunction with a hedgehog inhibitor and/or Connaught Medical Research Labs medium (CRML medium) (Invitrogen, Carlsbad, Calif.). In especially preferred embodiments, FGF-10 and/or KAAD-cyclopamine is provided to a cell culture comprising PDX1-negative definitive endoderm cells in the absence of RA or other retinoid. In certain embodiments, BMP4 may be included in FGF-10 and/or KAAD-cyclopamine in the absence of RA or other retinoid. After about one day to about ten days subsequent to the addition of the FGF-family growth factor analog or mimetic and/or hedgehog inhibitor, a retinoid, such as RA, or a retinoid containing supplement, such as B27, is provided to induce the expression of PDX1. In a preferred embodiments, RA is provided at about 2 days, about 3 day, about 4 day or about 5 days subsequent to the addition of the FGF-family growth factor analog or mimetic and/or hedgehog inhibitor. In other embodiments, B27 is provided at about the same time as providing the FGF-family growth factor analog or mimetic and/or hedgehog inhibitor.

With respect to some of the embodiments of differentiation processes described herein, a retinoid and a combination of the above-mentioned differentiation factors are provided to the cells so that these factors are present in the cell culture or cell population at concentrations sufficient to promote differentiation of at least a portion of the PDX1-negative definitive endoderm cell culture or cell population to ventral PDX1-positive foregut endoderm cells. When used in connection with cell cultures and/or cell populations, the term “portion” means any non-zero amount of the cell culture or cell population, which ranges from a single cell to the entirety of the cell culture or cell population. In preferred embodiments, the term “portion” means at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 11%, at least 12%, at least 13%, at least 14%, at least 15%, at least 16%, at least 17%, at least 18%, at least 19%, at least 20%, at least 21%, at least 22%, at least 23%, at least 24%, at least 25%, at least 26%, at least 27%, at least 28%, at least 29%, at least 30%, at least 31%, at least 32%, at least 33%, at least 34%, at least 35%, at least 36%, at least 37%, at least 38%, at least 39%, at least 40%, at least 41%, at least 42%, at least 43%, at least 44%, at least 45%, at least 46%, at least 47%, at least 48%, at least 49%, at least 50%, at least 51%, at least 52%, at least 53%, at least 54%, at least 55%, at least 56%, at least 57%, at least 58%, at least 59%, at least 60%, at least 61%, at least 62%, at least 63%, at least 64%, at least 65%, at least 66%, at least 67%, at least 68%, at least 69%, at least 70%, at least 71%, at least 72%, at least 73%, at least 74% or at least 75% of the cell culture or cell population.

In some embodiments of the present invention, the FGF-family growth factor or FGF-family growth factor analog or mimetic is provided to the cells of a cell culture such that it is present at a concentration of at least about 10 ng/ml, at least about 25 ng/ml, at least about 50 ng/ml, at least about 75 ng/ml, at least about 100 ng/ml, at least about 200 ng/ml, at least about 300 ng/ml, at least about 400 ng/ml, at least about 500 ng/ml, or at least about 1000 ng/ml. In other embodiments, when used alone or in conjunction with FGF-10, KAAD-cyclopamine can be provided at a concentration of at least about 0.01 μM, at least about 0.02 μM, at least about 0.04 μM, at least about 0.08 μM, at least about 0.1 μM, at least about 0.2 μM, at least about 0.3 μM, at least about 0.4 μM, at least about 0.5 μM, at least about 0.6 μM, at least about 0.7 μM, at least about 0.8 μM, at least about 0.9 μM, at least about 1 μM, at least about 1.1 μM, at least about 1.2 μM, at least about 1.3 μM, at least about 1.4 μM, at least about 1.5 μM, at least about 1.6 μM, at least about 1.7 μM, at least about 1.8 μM, at least about 1.9 μM, at least about 2 μM, at least about 2.1 μM, at least about 2.2 μM, at least about 2.3 μM, at least about 2.4 μM, at least about 2.5 μM, at least about 2.6 μM, at least about 2.7 μM, at least about 2.8 μM, at least about 2.9 μM, at least about 3 μM, at least about 3.5 μM, at least about 4 μM, at least about 4.5 μM, at least about 5 μM, at least about 10 μM, at least about 20 μM, at least about 30 μM, at least about 40 μM or at least about 50 μM.

In preferred embodiments of the present invention, a population of ventrally-biased PDX1-positive foregut endoderm cells is produced by providing a population of PDX1-negative definitive endoderm with 50 ng/ml of FGF-10 and 0.5 μM KAAD-cyclopamine in CMRL medium in the absence of RA. About two days subsequent to the addition of FGF-10 and KAAD-cyclopamine 2 μM RA is added to complete the differentiation of the cells to PDX1-positive cells.

In some embodiments, the differentiation factors and/or CRML medium is provided to the PDX1-negative definitive endoderm cells at about three days, at about four days, at about five days, at about six days, at about seven days, at about eight days, at about nine days, at about ten days or at about greater than ten days subsequent to the initiation of differentiation from hESCs. In preferred embodiments, differentiation factors and/or CRML medium is provided to the PDX1-negative definitive endoderm cells at about three days subsequent to the initiation of differentiation from hESCs.

In certain embodiments of the present invention, the above-mentioned differentiation factors are removed from the cell culture subsequent to their addition. For example, the above-mentioned differentiation factors can be removed within about one day, about two days, about three days, about four days, about five days, about six days, about seven days, about eight days, about nine days or about ten days after their addition.

Cultures of ventral PDX1-positive foregut endoderm cells can be grown in a medium containing reduced serum. Serum concentrations can range from about 0.05% (v/v) to about 20% (v/v). In some embodiments, ventral PDX1-positive foregut endoderm cells are grown with serum replacement. For example, in certain embodiments, the serum concentration of the medium can be less than about 0.05% (v/v), less than about 0.1% (v/v), less than about 0.2% (v/v), less than about 0.3% (v/v), less than about 0.4% (v/v), less than about 0.5% (v/v), less than about 0.6% (v/v), less than about 0.7% (v/v), less than about 0.8% (v/v), less than about 0.9% (v/v), less than about 1% (v/v), less than about 2% (v/v), less than about 3% (v/v), less than about 4% (v/v), less than about 5% (v/v), less than about 6% (v/v), less than about 7% (v/v), less than about 8% (v/v), less than about 9% (v/v), less than about 10% (v/v), less than about 15% (v/v) or less than about 20% (v/v). In some embodiments, ventral PDX1-positive foregut endoderm cells are grown without serum. In other embodiments, ventral PDX1-positive foregut endoderm cells are grown with serum replacement.

In still other embodiments, ventral PDX1-positive foregut endoderm cells are grown in the presence of B27. In such embodiments, B27 can be provided to the culture medium in concentrations ranging from about 0.1% (v/v) to about 20% (v/v) or in concentrations greater than about 20% (v/v). In certain embodiments, the concentration of B27 in the medium is about 0.1% (v/v), about 0.2% (v/v), about 0.3% (v/v), about 0.4% (v/v), about 0.5% (v/v), about 0.6% (v/v), about 0.7% (v/v), about 0.8% (v/v), about 0.9% (v/v), about 1% (v/v), about 2% (v/v), about 3% (v/v), about 4% (v/v), about 5% (v/v), about 6% (v/v), about 7% (v/v), about 8% (v/v), about 9% (v/v), about 10% (v/v), about 15% (v/v) or about 20% (v/v). Alternatively, the concentration of the added B27 supplement can be measured in terms of multiples of the strength of a commercially available B27 stock solution. For example, B27 is available from Invitrogen (Carlsbad, Calif.) as a 50X stock solution. Addition of a sufficient amount of this stock solution to a sufficient volume of growth medium produces a medium supplemented with the desired amount of B27. For example, the addition of 10 ml of 50X B27 stock solution to 90 ml of growth medium would produce a growth medium supplemented with 5X B27. The concentration of B27 supplement in the medium can be about 0.1X, about 0.2X, about 0.3X, about 0.4X, about 0.5X, about 0.6X, about 0.7X, about 0.8X, about 0.9X, about 1X, about 1.1X, about 1.2X, about 1.3X, about 1.4X, about 1.5X, about 1.6X, about 1.7X, about 1.8X, about 1.9X, about 2X, about 2.5X, about 3X, about 3.5X, about 4X, about 4.5X, about 5X, about 6X, about 7X, about 8X, about 9X, about 10X, about 11X, about 12X, about 13X, about 14X, about 15X, about 16X, about 17X, about 18X, about 19X, about 20X and greater than about 20X. In some embodiments where B27 is provided, a retinoid is not provided to complete the differentiation of the PDX1-negative cells to ventral PDX1-positive foregut endoderm.

Monitoring the Differentiation of PDX1-Negative Definitive Endoderm to PDX1-Positive Foregut Endoderm

As with the differentiation of definitive endoderm cells from pluripotent cells, the progression of differentiation from PDX1-negative, SOX17-positive definitive endoderm to PDX1-positive foregut endoderm can be monitored by determining the expression of markers characteristic of these cell types. Such monitoring permits one to determine the amount of time that is sufficient for the production of a desired amount of PDX1-positive foregut endoderm under various conditions, for example, one or more differentiation factor concentrations and environmental conditions. In preferred embodiments, the amount of time that is sufficient for the production of a desired amount of PDX1-positive foregut endoderm is determined by detecting the expression of PDX1. In some embodiments of the present invention, the expression of certain markers is determined by detecting the presence or absence of the marker. Alternatively, the expression of certain markers can be determined by measuring the level at which the marker is present in the cells of the cell culture or cell population. In such embodiments, the measurement of marker expression can be qualitative or quantitative. As described above, a preferred method of quantitating the expression markers that are produced by marker genes is through the use of Q-PCR. In particular embodiments, Q-PCR is used to monitor the progression of cells of the PDX1-negative, SOX17-positive definitive endoderm culture to PDX1-positive foregut endoderm cells by quantitating expression of marker genes characteristic of PDX1-positive foregut endoderm and the lack of expression of marker genes characteristic of other cell types. Other methods which are known in the art can also be used to quantitate marker gene expression. For example, the expression of a marker gene product can be detected by using antibodies specific for the marker gene product of interest. In some embodiments of the present invention, the expression of marker genes characteristic of PDX1-positive foregut endoderm as well as the lack of significant expression of marker genes characteristic of PDX1-negative definitive endoderm, hESCs and other cell types is determined.

As described further in the Examples below, PDX1 is a marker gene that is associated with PDX1-positive foregut endoderm. As such, in some embodiments of the present invention, the expression of PDX1 is determined. In other embodiments, the expression of other markers, which are expressed in PDX1-positive foregut endoderm, including, but not limited to, SOX17, HOXA13 and/or HOXC6 is also determined. Since PDX1 can also be expressed by certain other cell types (that is, visceral endoderm and certain neural ectoderm), some embodiments of the present invention relate to demonstrating the absence or substantial absence of marker gene expression that is associated with visceral endoderm and/or neural ectoderm. For example, in some embodiments, the expression of markers, which are expressed in visceral endoderm and/or neural cells, including, but not limited to, SOX7, AFP, SOX1, ZIC1 and/or NFM is determined.

In some embodiments, PDX1-positive foregut endoderm cell cultures produced by the methods described herein are substantially free of cells expressing the SOX7, AFP, SOX1, ZIC1 or NFM marker genes. In certain embodiments, the PDX1-positive foregut endoderm cell cultures produced by the processes described herein are substantially free of visceral endoderm, parietal endoderm and/or neural cells.

Monitoring the Differentiation of PDX1-Negative Definitive Endoderm to Dorsal PDX1-Positive Foregut Endoderm

Expression of one or more of the markers described in Table 3 and/or Table 4, in the Examples below, can be detected and/or quantitated using the above-described methods, such as Q-PCR and/or immunocytochemistry, to monitor the differentiation of PDX1-negative definitive endoderm to dorsal PDX1-positive endoderm. Markers associated with both dorsally-biased and ventrally-biased PDX1-positive foregut endoderm cells are described in Table 3. Of these markers, the markers selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2 and SLC27A2 are cell surface markers. Some preferred markers listed in Table 3 for monitoring the production of dorsal PDX1-positive foregut endoderm are selected from the group consisting of SERPINF2, DUSP9, CDH6 and SOX9. Markers associated with dorsally-biased foregut endoderm are described in Table 4. Each of the Table 4 markers is expressed preferentially, specifically or uniquely in dorsal PDX1-positive foregut endoderm cells as compared to other PDX1-positive cells. Of these markers, the markers selected from the group consisting of ADORA2A, CD47, EPB41L1, MAG, SFRP5, SLC16A10, SLC16A2, SLC1A3, SLC30A4, SLICK, SLITRK4 and XPR1 are cell surface markers. Some preferred markers listed in Table 4 for monitoring the production of dorsal PDX1-positive foregut endoderm are selected from the group consisting of HOXA1, PDE11A, FAM49A and WNT5A.

In addition to the above-described markers, in some embodiments of the present invention, the expression of other markers, which are expressed in PDX1-positive foregut endoderm, including, but not limited to, SOX17, HOXA13 and/or HOXC6 is also determined. Since PDX1 can also be expressed by certain other cell types (that is, visceral endoderm and certain neural ectoderm), some embodiments of the present invention relate to demonstrating the absence or substantial absence of marker gene expression that is associated with visceral endoderm and/or neural ectoderm. For example, in some embodiments, the expression of markers, which are expressed in visceral endoderm and/or neural cells, including, but not limited to, S OX7, AFP, S OX1, ZIC1 and/or NFM is determined.

In some embodiments, dorsal PDX1-positive foregut endoderm cell cultures produced by the methods described herein are substantially free of cells expressing the SOX7, AFP, SOX1, ZIC1 or NFM marker genes. In certain embodiments, the dorsal PDX1-positive foregut endoderm cell cultures produced by the processes described herein are substantially free of visceral endoderm, parietal endoderm and/or neural cells.

Monitoring the Differentiation of PDX1-Negative Definitive Endoderm to Ventral PDX1-Positive Foregut Endoderm

As described in the previous section, markers associated with both dorsally-biased and ventrally-biased PDX1-positive foregut endoderm cells are described in Table 3. As such, expression of one or more of the markers described in Table 3 can be detected and/or quantitated using the above-described methods, such as Q-PCR and/or immunocytochemistry, to monitor the differentiation of PDX1-negative definitive endoderm to ventral PDX1-positive endoderm. Of the markers described in Table 3, the markers selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2 and SLC27A2 are cell surface markers. Some preferred markers listed in Table 3 for monitoring the production of ventral PDX1-positive foregut endoderm are selected from the group consisting of SERPINF2, DUSP9, CDH6 and SOX9. Furthermore, because the markers described in Table 4 are preferentially, specifically or uniquely expressed in dorsally-biased foregut endoderm, detecting the lack of expression, or reduced expression relative to the expression in dorsal PDX1-positive foregut endoderm, of one or more of these markers is also useful for monitoring the differentiation of PDX1-negative definitive endoderm to ventral PDX1-positive foregut endoderm. Of the Table 4 markers, the markers selected from the group consisting of ADORA2A, CD47, EPB41L1, MAG, SFRP5, SLC16A10, SLC16A2, SLC1A3, SLC30A4, SLICK, SLITRK4 and XPR1 are cell surface markers. Some preferred markers listed in Table 4 for monitoring the production of dorsal PDX1-positive foregut endoderm are selected from the group consisting of HOXA1, PDE11A, FAM49A and WNT5A. As such, the absence, or insubstantial expression, of these markers in PDX1-positive cells expressing one or more markers selected from Table 3, is indicative of ventral PDX1-positive

In addition to the above-described markers, in some embodiments of the present invention, the expression of other markers, which are expressed in PDX1-positive foregut endoderm, including, but not limited to, SOX17, HOXA13 and/or HOXC6 is also determined. Since PDX1 can also be expressed by certain other cell types (that is, visceral endoderm and certain neural ectoderm), some embodiments of the present invention relate to demonstrating the absence or substantial absence of marker gene expression that is associated with visceral endoderm and/or neural ectoderm. For example, in some embodiments, the expression of markers, which are expressed in visceral endoderm and/or neural cells, including, but not limited to, SOX7, AFP, SOX1, ZIC1 and/or NFM is determined.

In some embodiments, ventral PDX1-positive foregut endoderm cell cultures produced by the methods described herein are substantially free of cells expressing the SOX7, AFP, SOX1, ZIC1 or NFM marker genes. In certain embodiments, the ventral PDX1-positive foregut endoderm cell cultures produced by the processes described herein are substantially free of visceral endoderm, parietal endoderm and/or neural cells.

Enrichment, Isolation and/or Purification of Dorsal and/or Ventral PDX1-Positive Foregut Endoderm

PDX1-positive foregut endoderm cells, including dorsal and/or ventral PDX1-positive foregut endoderm cells, produced by any of the above-described processes can be enriched, isolated and/or purified by using an affinity tag that is specific for such cells. Examples of affinity tags specific for dorsal and/or ventral PDX1-positive foregut endoderm cells are antibodies, ligands or other binding agents that are specific to a marker molecule, such as a polypeptide, that is present on the cell surface of dorsal and/or ventral PDX1-positive foregut endoderm cells but which is not substantially present on other cell types that would be found in a cell culture produced by the methods described herein. In some processes, an antibody which binds to a cell surface marker selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2, SLC27A2, ADORA2A, CD47, EPB41L1, MAG, SFRP5, SLC16A10, SLC16A2, SLC1A3, SLC30A4, SLICK, SLITRK4 and XPR1 is used as an affinity tag for the enrichment, isolation or purification of dorsal and/or ventral PDX1-positive foregut endoderm cells.

Methods for making antibodies and using them for cell isolation are known in the art and such methods can be implemented for use with the antibodies and dorsal and/or ventral PDX1-positive foregut endoderm cells described herein. In one process, an antibody which binds to a marker selected from CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2, SLC27A2, ADORA2A, CD47, EPB41L1, MAG, SFRP5, SLC16A10, SLC16A2, SLC1A3, SLC30A4, SLICK, SLITRK4 and XPR1 is attached to a magnetic bead and then allowed to bind to dorsal and/or ventral PDX1-positive foregut endoderm cells in a cell culture which has been enzymatically treated to reduce intercellular and substrate adhesion. The cell/antibody/bead complexes are then exposed to a movable magnetic field which is used to separate bead-bound definitive endoderm cells from unbound cells. Once the dorsal and/or ventral PDX1-positive foregut endoderm cells are physically separated from other cells in culture, the antibody binding is disrupted and the cells are replated in appropriate tissue culture medium.

Additional methods for obtaining enriched, isolated or purified dorsal and/or ventral PDX1-positive foregut endoderm cell cultures or populations can also be used. For example, in some embodiments, an antibody that binds to a marker selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2, SLC27A2, ADORA2A, CD47, EPB41L1, MAG, SFRP5, SLC16A10, SLC16A2, SLC1A3, SLC30A4, SLICK, SLITRK4 and XPR1 is incubated with a dorsal and/or ventral PDX1-positive foregut endoderm-containing cell culture that has been treated to reduce intercellular and substrate adhesion. The cells are then washed, centrifuged and resuspended. The cell suspension is then incubated with a secondary antibody, such as an FITC-conjugated antibody that is capable of binding to the primary antibody. The cells are then washed, centrifuged and resuspended in buffer. The cell suspension is then analyzed and sorted using a fluorescence activated cell sorter (FACS). The marker-positive cells are collected separately from marker-negative cells, thereby resulting in the isolation of such cell types. If desired, the isolated cell compositions can be further purified by using an alternate affinity-based method or by additional rounds of sorting using the same or different markers that are specific for dorsal and/or ventral PDX1-positive foregut endoderm cells.

In still other processes, dorsal and/or ventral PDX1-positive foregut endoderm cells are enriched, isolated and/or purified using a ligand or other molecule that binds to a marker selected from the group consisting of CDH6, GABRA2, GRIA3, IL6R, KCNJ2, LGALS3, LGALS3/GALIG, SERPINF2, SLC27A2, ADORA2A, CD47, EPB41L1, MAG, SFRP5, SLC16A10, SLC16A2, SLC1A3, SLC30A4, SLICK, SLITRK4 and XPR1.

In preferred processes, dorsal and/or ventral PDX1-positive foregut endoderm cells are enriched, isolated and/or purified from other cells after the PDX1-negative definitive endoderm cell cultures are induced to differentiate towards the dorsal and/or ventral PDX1-positive foregut endoderm lineage. It will be appreciated that the above-described enrichment, isolation and purification procedures can be used with such cultures at any stage of differentiation.

In addition to the procedures just described, dorsal and/or ventral PDX1-positive foregut endoderm cells may also be isolated by other techniques for cell isolation. Additionally, dorsal and/or ventral PDX1-positive foregut endoderm cells may also be enriched or isolated by methods of serial subculture in growth conditions which promote the selective survival or selective expansion of the dorsal and/or ventral PDX1-positive foregut endoderm cells.

Using the methods described herein, enriched, isolated and/or purified populations of dorsal and/or ventral PDX1-positive foregut endoderm cells and or tissues can be produced in vitro from PDX1-negative definitive endoderm cell cultures or cell populations, which have undergone at least some differentiation. In some methods, the cells undergo random differentiation. In a preferred method, however, the cells are directed to differentiate primarily into dorsal and/or ventral PDX1-positive foregut endoderm cells. Some preferred enrichment, isolation and/or purification methods relate to the in vitro production of dorsal and/or ventral PDX1-positive foregut endoderm cells from human PDX1-negative definitive endoderm cells. Using the methods described herein, cell populations or cell cultures can be enriched in dorsal and/or ventral PDX1-positive foregut endoderm content by at least about 2- to about 1000-fold as compared to untreated cell populations or cell cultures. In some embodiments, dorsal and/or ventral PDX1-positive foregut endoderm cells can be enriched by at least about 5- to about 500-fold as compared to untreated cell populations or cell cultures. In other embodiments, dorsal and/or ventral PDX1-positive foregut endoderm cells can be enriched from at least about 10- to about 200-fold as compared to untreated cell populations or cell cultures. In still other embodiments, dorsal and/or ventral PDX1-positive foregut endoderm cells can be enriched from at least about 20- to about 100-fold as compared to untreated cell populations or cell cultures. In yet other embodiments, dorsal and/or ventral PDX1-positive foregut endoderm cells can be enriched from at least about 40- to about 80-fold as compared to untreated cell populations or cell cultures. In certain embodiments, dorsal and/or ventral PDX1-positive foregut endoderm cells can be enriched from at least about 2- to about 20-fold as compared to untreated cell populations or cell cultures.

Enrichment, Isolation and/or Purification Of Dorsal and/or Ventral PDX1-Positive Foregut Endoderm

With respect to additional aspects of the present invention, dorsal and/or ventral PDX1-positive foregut endoderm cells can be enriched, isolated and/or purified. In some embodiments of the present invention, cell populations enriched for dorsal and/or ventral PDX1-positive foregut endoderm cells are produced by isolating such cells from cell cultures.

In some embodiments of the present invention, dorsal and/or ventral PDX1-positive foregut endoderm cells are fluorescently labeled then isolated from non-labeled cells by using a fluorescence activated cell sorter (FACS). In such embodiments, a nucleic acid encoding fluorescent protein (GFP) or another nucleic acid encoding an expressible fluorescent marker gene, such as the gene encoding luciferase, is used to label PDX1-positive cells. For example, in some embodiments, at least one copy of a nucleic acid encoding GFP or a biologically active fragment thereof is introduced into a pluripotent cell, preferably a human embryonic stem cell, downstream of the promoter of a gene selected from Table 3 or Table 4 such that the expression of the GFP gene product or biologically active fragment thereof is under control of the such promoter. In some embodiments, the entire coding region of the nucleic acid, which encodes the marker selected from Table 3 or Table 4, is replaced by a nucleic acid encoding GFP or a biologically active fragment thereof. In other embodiments, the nucleic acid encoding GFP or a biologically active fragment thereof is fused in frame with at least a portion of the nucleic acid encoding the marker selected from Table 3 or Table 4, thereby generating a fusion protein. In such embodiments, the fusion protein retains a fluorescent activity similar to GFP.

Fluorescently marked cells, such as the above-described pluripotent cells, are differentiated to definitive endoderm and then to dorsal and/or ventral PDX1-positive foregut endoderm cells as described previously above. Because dorsal and/or ventral PDX1-positive foregut endoderm cells express the fluorescent marker gene, whereas PDX1-negative cells do not, these two cell types can be separated. In some embodiments, cell suspensions comprising a mixture of fluorescently-labeled dorsal and/or ventral PDX1-positive foregut endoderm cells and unlabeled PDX1-negative cells are sorted using a FACS. Dorsal and/or ventral PDX1-positive foregut endoderm cells are collected separately from PDX1-negative cells, thereby resulting in the isolation of such cell types. If desired, the isolated cell compositions can be further purified by additional rounds of sorting using the same or different markers that are specific for dorsal and/or ventral PDX1-positive foregut endoderm.

It will be appreciated that the above-described enrichment, isolation and purification procedures can be used with such cultures at any stage of differentiation.

Using the methods described herein, enriched, isolated and/or purified populations of dorsal and/or ventral PDX1-positive foregut endoderm cells and/or tissues can be produced in vitro from PDX1-negative, SOX17-positive definitive endoderm cell cultures or cell populations which have undergone at least some differentiation. In some embodiments, the cells undergo random differentiation. In a preferred embodiment, however, the cells are directed to differentiate primarily into dorsal and/or ventral PDX1-positive foregut endoderm cells. Some preferred enrichment, isolation and/or purification methods relate to the in vitro production of dorsal and/or ventral PDX1-positive foregut endoderm cells from human embryonic stem cells.

Using the methods described herein, cell populations or cell cultures can be enriched in dorsal and/or ventral PDX1-positive foregut endoderm cell content by at least about 2- to about 1000-fold as compared to untreated cell populations or cell cultures. In some embodiments, dorsal and/or ventral PDX1-positive foregut endoderm cells can be enriched by at least about 5- to about 500-fold as compared to untreated cell populations or cell cultures. In other embodiments, dorsal and/or ventral PDX1-positive foregut endoderm cells can be enriched from at least about 10- to about 200-fold as compared to untreated cell populations or cell cultures. In still other embodiments, dorsal and/or ventral PDX1-positive foregut endoderm cells can be enriched from at least about 20- to about 100-fold as compared to untreated cell populations or cell cultures. In yet other embodiments, dorsal and/or ventral PDX1-positive foregut endoderm cells can be enriched from at least about 40- to about 80-fold as compared to untreated cell populations or cell cultures. In certain embodiments, dorsal and/or ventral PDX1-positive foregut endoderm cells can be enriched from at least about 2- to about 20-fold as compared to untreated cell populations or cell cultures.

Compositions Comprising Dorsal and/or Ventral PDX1-Positive Foregut Endoderm

Some embodiments of the present invention relate to cell compositions, such as cell cultures or cell populations, comprising dorsal and/or ventral PDX1-positive foregut endoderm cells, wherein the dorsal and/or ventral PDX1-positive foregut endoderm cells are multipotent cells that can differentiate into cells, tissues or organs derived from the anterior portion of the gut tube, such as the dorsal pancreatic bud and/or the ventral pancreatic bud. In accordance with certain embodiments, the dorsal and/or ventral PDX1-positive foregut endoderm cells are mammalian cells, and in a preferred embodiment, such cells are human cells.

Other embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising cells of one or more cell types selected from the group consisting of hESCs, PDX1-negative definitive endoderm cells, dorsal and/or ventral PDX1-positive foregut endoderm cells and mesoderm cells. In some embodiments, hESCs comprise less than about 5%, less than about 4%, less than about 3%, less than about 2% or less than about 1% of the total cells in the culture. In other embodiments, PDX1-negative definitive endoderm cells comprise less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 12%, less than about 10%, less than about 8%, less than about 6%, less than about 5%, less than about 4%, less than about 3%, less than about 2% or less than about 1% of the total cells in the culture. In yet other embodiments, mesoderm cells comprise less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 12%, less than about 10%, less than about 8%, less than about 6%, less than about 5%, less than about 4%, less than about 3%, less than about 2% or less than about 1% of the total cells in the culture.

Additional embodiments of the present invention relate to compositions, such as cell cultures or cell populations, produced by the processes described herein comprise dorsal and/or ventral PDX1-positive foregut endoderm as the majority cell type. In some embodiments, the processes described herein produce cell cultures and/or cell populations comprising at least about 99%, at least about 98%, at least about 97%, at least about 96%, at least about 95%, at least about 94%, at least about 93%, at least about 92%, at least about 91%, at least about 90%, at least about 89%, at least about 88%, at least about 87%, at least about 86%, at least about 85%, at least about 84%, at least about 83%, at least about 82%, at least about 81%, at least about 80%, at least about 79%, at least about 78%, at least about 77%, at least about 76%, at least about 75%, at least about 74%, at least about 73%, at least about 72%, at least about 71%, at least about 70%, at least about 69%, at least about 68%, at least about 67%, at least about 66%, at least about 65%, at least about 64%, at least about 63%, at least about 62%, at least about 61%, at least about 60%, at least about 59%, at least about 58%, at least about 57%, at least about 56%, at least about 55%, at least about 54%, at least about 53%, at least about 52%, at least about 51% or at least about 50% dorsal and/or ventral PDX1-positive foregut endoderm cells. In preferred embodiments the cells of the cell cultures or cell populations comprise human cells. In other embodiments, the processes described herein produce cell cultures or cell populations comprising at least about 50%, at least about 45%, at least about 40%, at least about 35%, at least about 30%, at least about 25%, at least about 24%, at least about 23%, at least about 22%, at least about 21%, at least about 20%, at least about 19%, at least about 18%, at least about 17%, at least about 16%, at least about 15%, at least about 14%, at least about 13%, at least about 12%, at least about 11%, at least about 10%, at least about 9%, at least about 8%, at least about 7%, at least about 6%, at least about 5%, at least about 4%, at least about 3%, at least about 2% or at least about 1% dorsal and/or ventral PDX1-positive foregut endoderm cells. In preferred embodiments, the cells of the cell cultures or cell populations comprise human cells. In some embodiments, the percentage of dorsal and/or ventral PDX1-positive foregut endoderm cells in the cell cultures or populations is calculated without regard to the feeder cells remaining in the culture.

Still other embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising mixtures of dorsal and/or ventral PDX1-positive foregut endoderm cells and PDX1-negative definitive endoderm cells. For example, cell cultures or cell populations comprising at least about 5 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 95 PDX1-negative definitive endoderm cells can be produced. In other embodiments, cell cultures or cell populations comprising at least about 95 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 5 PDX1-negative definitive endoderm cells can be produced. Additionally, cell cultures or cell populations comprising other ratios of dorsal and/or ventral PDX1-positive foregut endoderm cells to PDX1-negative definitive endoderm cells are contemplated. For example, compositions comprising at least about 1 dorsal or ventral PDX1-positive foregut endoderm cell for about every 1,000,000 PDX1-negative definitive endoderm cells, at least about 1 dorsal or ventral PDX1-positive foregut endoderm cell for about every 100,000 PDX1-negative definitive endoderm cells, at least about 1 dorsal or ventral PDX1-positive foregut endoderm cell for about every 10,000 PDX1-negative definitive endoderm cells, at least about 1 dorsal or ventral PDX1-positive foregut endoderm cell for about every 1000 PDX1-negative definitive endoderm cells, at least about 1 dorsal or ventral PDX1-positive foregut endoderm cell for about every 500 PDX1-negative definitive endoderm cells, at least about 1 dorsal or ventral PDX1-positive foregut endoderm cell for about every 100 PDX1-negative definitive endoderm cells, at least about 1 dorsal or ventral PDX1-positive foregut endoderm cell for about every 10 PDX1-negative definitive endoderm cells, at least about 1 dorsal or ventral PDX1-positive foregut endoderm cell for about every 5 PDX1-negative definitive endoderm cells, at least about 1 dorsal or ventral PDX1-positive foregut endoderm cell for about every 4 PDX1-negative definitive endoderm cells, at least about 1 dorsal or ventral PDX1-positive foregut endoderm cell for about every 2 PDX1-negative definitive endoderm cells, at least about 1 dorsal or ventral PDX1-positive foregut endoderm cell for about every 1 PDX1-negative definitive endoderm cell, at least about 2 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 4 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 5 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 10 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 20 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 50 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 100 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 1000 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 10,000 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell, at least about 100,000 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell and at least about 1,000,000 dorsal and/or ventral PDX1-positive foregut endoderm cells for about every 1 PDX1-negative definitive endoderm cell are contemplated.

In some embodiments of the present invention, the PDX1-negative definitive endoderm cells from which dorsal and/or ventral PDX1-positive foregut endoderm cells are produced are derived from human pluripotent cells, such as human pluripotent stem cells. In certain embodiments, the human pluripotent cells are derived from a morula, the inner cell mass of an embryo or the gonadal ridges of an embryo. In certain other embodiments, the human pluripotent cells are derived from the gonadal or germ tissues of a multicellular structure that has developed past the embryonic stage.

Further embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising human cells, including human dorsal and/or ventral PDX1-positive foregut endoderm cells, wherein the expression of the PDX1 marker is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 2% of the human cells. In other embodiments, the expression of the PDX1 marker is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 5% of the human cells, in at least about 10% of the human cells, in at least about 15% of the human cells, in at least about 20% of the human cells, in at least about 25% of the human cells, in at least about 30% of the human cells, in at least about 35% of the human cells, in at least about 40% of the human cells, in at least about 45% of the human cells, in at least about 50% of the human cells, in at least about 55% of the human cells, in at least about 60% of the human cells, in at least about 65% of the human cells, in at least about 70% of the human cells, in at least about 75% of the human cells, in at least about 80% of the human cells, in at least about 85% of the human cells, in at least about 90% of the human cells, in at least about 95% of the human cells or in at least about 98% of the human cells. In some embodiments, the percentage of human cells in the cell cultures or populations, wherein the expression of PDX1 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker, is calculated without regard to feeder cells.

It will be appreciated that some embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising human dorsal and/or ventral PDX1-positive foregut endoderm cells, wherein the expression of one or more markers selected from the group consisting of SOX17, HOXA13 and HOXC6 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in from at least about 2% to greater than at least about 98% of the human cells. In some embodiments, the expression of one or more markers selected from the group consisting of SOX17, HOXA13 and HOXC6 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 5% of the human cells, in at least about 10% of the human cells, in at least about 15% of the human cells, in at least about 20% of the human cells, in at least about 25% of the human cells, in at least about 30% of the human cells, in at least about 35% of the human cells, in at least about 40% of the human cells, in at least about 45% of the human cells, in at least about 50% of the human cells, in at least about 55% of the human cells, in at least about 60% of the human cells, in at least about 65% of the human cells, in at least about 70% of the human cells, in at least about 75% of the human cells, in at least about 80% of the human cells, in at least about 85% of the human cells, in at least about 90% of the human cells, in at least about 95% of the human cells or in at least about 98% of the human cells. In some embodiments, the percentage of human cells in the cell cultures or populations, wherein the expression of one or more markers selected from the group consisting of SOX17, HOXA13 and HOXC6 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker, is calculated without regard to feeder cells.

Other embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising human cells, including human dorsal and/or ventral PDX1-positive foregut endoderm cells, wherein the expression of one or more markers selected from Table 3 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 2% of the human cells. In other embodiments, the expression of the one or more markers selected from Table 3 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 5% of the human cells, in at least about 10% of the human cells, in at least about 15% of the human cells, in at least about 20% of the human cells, in at least about 25% of the human cells, in at least about 30% of the human cells, in at least about 35% of the human cells, in at least about 40% of the human cells, in at least about 45% of the human cells, in at least about 50% of the human cells, in at least about 55% of the human cells, in at least about 60% of the human cells, in at least about 65% of the human cells, in at least about 70% of the human cells, in at least about 75% of the human cells, in at least about 80% of the human cells, in at least about 85% of the human cells, in at least about 90% of the human cells, in at least about 95% of the human cells or in at least about 98% of the human cells. In some embodiments, the percentage of human cells in the cell cultures or populations, wherein the expression of one or more markers selected from Table 3 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker, is calculated without regard to feeder cells.

Other embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising human cells, including human dorsal PDX1-positive foregut endoderm cells, wherein the expression of one or more markers selected from Table 4 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 2% of the human cells. In other embodiments, the expression of the one or more markers selected from Table 4 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 5% of the human cells, in at least about 10% of the human cells, in at least about 15% of the human cells, in at least about 20% of the human cells, in at least about 25% of the human cells, in at least about 30% of the human cells, in at least about 35% of the human cells, in at least about 40% of the human cells, in at least about 45% of the human cells, in at least about 50% of the human cells, in at least about 55% of the human cells, in at least about 60% of the human cells, in at least about 65% of the human cells, in at least about 70% of the human cells, in at least about 75% of the human cells, in at least about 80% of the human cells, in at least about 85% of the human cells, in at least about 90% of the human cells, in at least about 95% of the human cells or in at least about 98% of the human cells. In some embodiments, the percentage of human cells in the cell cultures or populations, wherein the expression of one or more markers selected from Table 4 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker, is calculated without regard to feeder cells.

Other embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising human cells, including human ventral PDX1-positive foregut endoderm cells, wherein the expression of a marker selected from Table 3 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 2% of the human cells, and wherein a marker selected from Table 4 is not substantially expressed as compared to the expression of the same marker in dorsal PDX1-positive foregut endoderm cells. In other embodiments, the expression of the marker selected from Table 3 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 5% of the human cells, in at least about 10% of the human cells, in at least about 15% of the human cells, in at least about 20% of the human cells, in at least about 25% of the human cells, in at least about 30% of the human cells, in at least about 35% of the human cells, in at least about 40% of the human cells, in at least about 45% of the human cells, in at least about 50% of the human cells, in at least about 55% of the human cells, in at least about 60% of the human cells, in at least about 65% of the human cells, in at least about 70% of the human cells, in at least about 75% of the human cells, in at least about 80% of the human cells, in at least about 85% of the human cells, in at least about 90% of the human cells, in at least about 95% of the human cells or in at least about 98% of the human cells. In such embodiments, a marker selected from Table 4 is not substantially expressed as compared to the expression of the same marker in dorsal PDX1-positive foregut endoderm cells. In some embodiments, the percentage of human cells in the cell cultures or populations, wherein the expression of a marker selected from Table 3 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker, and wherein a marker selected from Table 4 is not substantially expressed as compared to the expression of the same marker in dorsal PDX1-positive foregut endoderm cells, is calculated without regard to feeder cells.

Additional embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising mammalian endodermal cells, such as human endoderm cells, wherein the expression of the PDX1 marker and the expression of one or more markers selected from Table 3 or Table 4 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 2% of the endodermal cells. In other embodiments, the expression of the PDX1 marker and the expression of one or more markers selected from Table 3 or Table 4 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 5% of the endodermal cells, in at least about 10% of the endodermal cells, in at least about 15% of the endodermal cells, in at least about 20% of the endodermal cells, in at least about 25% of the endodermal cells, in at least about 30% of the endodermal cells, in at least about 35% of the endodermal cells, in at least about 40% of the endodermal cells, in at least about 45% of the endodermal cells, in at least about 50% of the endodermal cells, in at least about 55% of the endodermal cells, in at least about 60% of the endodermal cells, in at least about 65% of the endodermal cells, in at least about 70% of the endodermal cells, in at least about 75% of the endodermal cells, in at least about 80% of the endodermal cells, in at least about 85% of the endodermal cells, in at least about 90% of the endodermal cells, in at least about 95% of the endodermal cells or in at least about 98% of the endodermal cells.

Still other embodiments of the present invention relate to compositions, such as cell cultures or cell populations, comprising mammalian endodermal cells, such as human endodermal cells, wherein the expression of one or more markers selected from the group consisting of SOX17, HOXA13 and HOXC6 and the expression of one or more markers selected from Table 3 or Table 4 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 2% of the endodermal cells. In other embodiments, the expression of one or more markers selected from the group consisting of SOX17, HOXA13 and HOXC6 and the expression of one or more markers selected from Table 3 or Table 4 is greater than the expression of the AFP, SOX7, SOX1, ZIC1 and/or NFM marker in at least about 5% of the endodermal cells, in at least about 10% of the endodermal cells, in at least about 15% of the endodermal cells, in at least about 20% of the endodermal cells, in at least about 25% of the endodermal cells, in at least about 30% of the endodermal cells, in at least about 35% of the endodermal cells, in at least about 40% of the endodermal cells, in at least about 45% of the endodermal cells, in at least about 50% of the endodermal cells, in at least about 55% of the endodermal cells, in at least about 60% of the endodermal cells, in at least about 65% of the endodermal cells, in at least about 70% of the endodermal cells, in at least about 75% of the endodermal cells, in at least about 80% of the endodermal cells, in at least about 85% of the endodermal cells, in at least about 90% of the endodermal cells, in at least about 95% of the endodermal cells or at least about 98% of the endodermal cells.

Using the processes described herein, compositions comprising dorsal and/or ventral PDX1-positive foregut endoderm cells substantially free of other cell types can be produced. With respect to cells in cell cultures or in cell populations, the term “substantially free of” means that the specified cell type of which the cell culture or cell population is free, is present in an amount of less than about 5% of the total number of cells present in the cell culture or cell population. In some embodiments of the present invention, the dorsal and/or ventral PDX1-positive foregut endoderm cell populations or cell cultures produced by the methods described herein are substantially free of cells that significantly express the AFP, SOX7, SOX1, ZIC1 and/or NFM marker genes.

In one embodiment of the present invention, a description of a dorsal PDX1-positive foregut endoderm cell based on the expression of marker genes is, PDX1 high, a marker selected from Table 3 high, a marker selected from Table 4 high, AFP low, SOX7 low, SOX1 low, ZIC1 low and NFM low.

In one embodiment of the present invention, a description of a ventral PDX1-positive foregut endoderm cell based on the expression of marker genes is, PDX1 high, a marker selected from Table 3 high, a marker selected from Table 4 low as compared to the expression of the same marker in dorsal PDX1-positive foregut endoderm, AFP low, SOX7 low, SOX1 low, ZIC1 low and NFM low.

Increasing Expression of Pdx1 in A Sox17-Positive Definitive Endoderm Cell

Some aspects of the present invention are related to methods of increasing the expression of the PDX1 gene product in cell cultures or cell populations comprising SOX17-positive definitive endoderm cells. In such embodiments, the SOX17-positive definitive endoderm cells are contacted with a differentiation factor in an amount that is sufficient to increase the expression of the PDX1 gene product. The SOX17-positive definitive endoderm cells that are contacted with the differentiation factor can be either PDX1-negative or PDX1-positive. In some embodiments, the differentiation factor can be a retinoid. In certain embodiments, SOX17-positive definitive endoderm cells are contacted with a retinoid at a concentration ranging from about 0.01 μM to about 50 μM. In a preferred embodiment, the retinoid is RA.

In other embodiments of the present invention, the expression of the PDX1 gene product in cell cultures or cell populations comprising SOX17-positive definitive endoderm cells is increased by contacting the SOX17-positive cells with a differentiation factor of the fibroblast growth factor family Such differentiation factors can either be used alone or in conjunction with RA. In some embodiments, the SOX17-positive definitive endoderm cells are contacted with a fibroblast growth factor at a concentration ranging from about 10 ng/ml to about 1000 ng/ml. In a preferred embodiment, the FGF growth factor is FGF-10.

In some embodiments of the present invention, the expression of the PDX1 gene product in cell cultures or cell populations comprising SOX17-positive definitive endoderm cells is increased by contacting the SOX17-positive cells with B27. This differentiation factor can either be used alone or in conjunction with one or both of retinoid and FGF family differentiation factors. In some embodiments, the SOX17-positive definitive endoderm cells are contacted with B27 at a concentration ranging from about 0.1% (v/v) to about 20% (v/v). In a preferred embodiment, the SOX17-positive definitive endoderm cells are contacted with RA, FGF-10 and B27.

Methods for increasing the expression of the PDX1 gene product in cell cultures or cell populations comprising SOX17-positive definitive endoderm cells can be carried out in growth medium containing reduced or no serum. In some embodiments, serum concentrations range from about 0.05% (v/v) to about 20% (v/v). In some embodiments, the SOX17-positive cells are grown with serum replacement.

It will be appreciated that the above described methods can also be used to increase the expression of one or more markers selected from Table 3 and/or Table 4 in dorsal PDX1-positive foregut endoderm cells. Similarly, such methods can be used to increase the expression of one or more markers selected from Table 3 in ventral PDX1-positive foregut endoderm cells.

Identification of Factors Capable of Promoting the Differentiation of PDX1-Negative Definitive Endoderm Cells to PDX1-Positive Foregut Endoderm Cells

Additional aspects of the present invention relate to methods of identifying one or more differentiation factors capable of promoting the differentiation of PDX1-negative definitive endoderm cells to PDX1-positive foregut endoderm cells. In such methods, a cell culture or cell population comprising PDX1-negative definitive endoderm cells is obtained and the expression of PDX1 in the cell culture or cell population is determined. After determining the expression of PDX1, the cells of the cell culture or cell population are contacted with a candidate differentiation factor. In some embodiments, the expression of PDX1 is determined at the time of contacting or shortly after contacting the cells with a candidate differentiation factor. PDX1 expression is then determined at one or more times after contacting the cells with the candidate differentiation factor. If the expression of PDX1 has increased after contact with the candidate differentiation factor as compared to PDX1 expression prior to contact with the candidate differentiation factor, the candidate differentiation factor is identified as capable of promoting the differentiation of PDX1-negative definitive endoderm cells to PDX1-positive foregut endoderm cells.

In some embodiments, the above-described methods of identifying factors capable of promoting the differentiation of PDX1-negative definitive endoderm cells to PDX1-positive foregut endoderm cells also include determining the expression of the HOXA13 gene and/or the HOXC6 gene in the cell culture or cell population. In such embodiments, the expression of HOXA13 and/or HOXC6 is determined both before and after the cells are contacted with the candidate differentiation factor. If the expression of PDX1 and HOXA13 has increased after contact with the candidate differentiation factor as compared to PDX1 and HOXA13 expression prior to contact with the candidate differentiation factor, the candidate differentiation factor is identified as capable of promoting the differentiation of PDX1-negative definitive endoderm cells to PDX1-positive foregut endoderm cells. Similarly, if the expression of PDX1 and HOXC6 has increased after contact with the candidate differentiation factor as compared to PDX1 and HOXC6 expression prior to contact with the candidate differentiation factor, the candidate differentiation factor is identified as capable of promoting the differentiation of PDX1-negative definitive endoderm cells to PDX1-positive foregut endoderm cells. In a preferred embodiment, a candidate differentiation factor is identified as being capable of promoting the differentiation of PDX1-negative definitive endoderm cells to PDX1-positive foregut endoderm cells by determining the expression of PDX1, HOXA13 and HOXC6 both before and after contacting the cells of the cell culture or cell population with the candidate differentiation factor. In preferred embodiments, the expression of PDX1, HOXA13 and/or HOXC6 is determined Q-PCR.

It will be appreciated that in some embodiments, the expression of one or more of PDX1, HOXA13 and HOXC6 can be determined at the time of contacting or shortly after contacting the cells of the cell cultures or cell populations with a candidate differentiation factor rather than prior to contacting the cells with a candidate differentiation factor. In such embodiments, the expression of one or more of PDX1, HOXA13 and HOXC6 at the time of contacting or shortly after contacting the cells with a candidate differentiation factor is compared to the expression of one or more of PDX1, HOXA13 and HOXC6 at one or more times after contacting the cells with a candidate differentiation factor.

In some embodiments of the above-described methods, the one or more times at which PDX1 expression is determined after contacting the cells with the candidate differentiation factor can range from about 1 hour to about 10 days. For example, PDX1 expression can be determined about 1 hour after contacting the cells with the candidate differentiation factor, about 2 hours after contacting the cells with the candidate differentiation factor, about 4 hours after contacting the cells with the candidate differentiation factor, about 6 hours after contacting the cells with the candidate differentiation factor, about 8 hours after contacting the cells with the candidate differentiation factor, about 10 hours after contacting the cells with the candidate differentiation factor, about 12 hours after contacting the cells with the candidate differentiation factor, about 16 hours after contacting the cells with the candidate differentiation factor, about 24 hours after contacting the cells with the candidate differentiation factor, about 2 days after contacting the cells with the candidate differentiation factor, about 3 days after contacting the cells with the candidate differentiation factor, about 4 days after contacting the cells with the candidate differentiation factor, about 5 days after contacting the cells with the candidate differentiation factor, about 6 days after contacting the cells with the candidate differentiation factor, about 7 days after contacting the cells with the candidate differentiation factor, about 8 days after contacting the cells with the candidate differentiation factor, about 9 days after contacting the cells with the candidate differentiation factor, about 10 days after contacting the cells with the candidate differentiation factor or more than 10 days after contacting the cells with the candidate differentiation factor.

Candidate differentiation factors for use in the methods described herein can be selected from compounds, such as polypeptides and small molecules. For example, candidate polypeptides can include, but are not limited to, growth factors, cytokines, chemokines, extracellular matrix proteins, and synthetic peptides. In a preferred embodiment, the growth factor is from the FGF family, for example FGF-10. Candidate small molecules include, but are not limited to, compounds generated from combinatorial chemical synthesis and natural products, such as steroids, isoprenoids, terpenoids, phenylpropanoids, alkaloids and flavinoids. It will be appreciated by those of ordinary skill in the art that thousands of classes of natural and synthetic small molecules are available and that the small molecules contemplated for use in the methods described herein are not limited to the classes exemplified above. Typically, small molecules will have a molecular weight less than 10,000 amu. In a preferred embodiment, the small molecule is a retinoid, for example RA.

It will be appreciated that the above-described methods can be used to identify factors capable of promoting the differentiation of PDX1-negative definitive endoderm cells to dorsal PDX1-positive foregut endoderm cells by monitoring the expression of one or more markers expression from Table 4. In some embodiments, the expression of one or more markers selected from Table 3 and one or more markers selected from Table 4 is monitored.

Similarly, it will also be appreciated that the above-described methods can be used to identify factors capable of promoting the differentiation of PDX1-negative definitive endoderm cells to ventral PDX1-positive foregut endoderm cells by monitoring the expression of one or more markers expression from Table 3. In some embodiments, the expression of one or more markers selected from Table 3 and one or more markers selected from Table 4 is monitored.

Identification of Factors Capable of Promoting the Differentiation of Dorsal and/or Ventral PDX1-Positive Foregut Endoderm Cells

Certain screening methods described herein relate to methods for identifying at least one differentiation factor that is capable of promoting the differentiation of dorsal and/or ventral PDX1-positive foregut endoderm cells. In some embodiments of these methods, cell populations comprising dorsal and/or ventral PDX1-positive foregut endoderm cells, such as human dorsal and/or ventral PDX1-positive foregut endoderm cells, are obtained. The cell population is then provided with a candidate differentiation factor. At a first time point, which is prior to or at approximately the same time as providing the candidate differentiation factor, expression of a marker is determined. Alternatively, expression of the marker can be determined after providing the candidate differentiation factor. At a second time point, which is subsequent to the first time point and subsequent to the step of providing the candidate differentiation factor to the cell population, expression of the same marker is again determined. Whether the candidate differentiation factor is capable of promoting the differentiation of the dorsal and/or ventral PDX1-positive foregut endoderm cells is determined by comparing expression of the marker at the first time point with the expression of the marker at the second time point. If expression of the marker at the second time point is increased or decreased as compared to expression of the marker at the first time point, then the candidate differentiation factor is capable of promoting the differentiation of dorsal and/or ventral PDX1-positive foregut endoderm cells. In preferred embodiments, expression of the marker is determined by Q-PCR.

Some embodiments of the screening methods described herein utilize cell populations or cell cultures which comprise human dorsal and/or ventral PDX1-positive foregut endoderm cells. For example, the cell population can be a substantially purified population of human dorsal and/or ventral PDX1-positive foregut endoderm cells. Alternatively, the cell population can be an enriched population of human dorsal and/or ventral PDX1-positive foregut endoderm cells, wherein at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97% or greater than at least about 97% of the human cells in the cell population are human dorsal and/or ventral PDX1-positive foregut endoderm cells. In other embodiments described herein, the cell population comprises human cells wherein at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85% or greater than at least about 85% of the human cells are human dorsal and/or ventral PDX1-positive foregut endoderm cells. In some embodiments, the cell population includes non-human cells such as non-human feeder cells. In other embodiments, the cell population includes human feeder cells. In such embodiments, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% or greater than at least about 95% of the human cells, other than said feeder cells, are human dorsal and/or ventral PDX1-positive foregut endoderm cells.

In embodiments of the screening methods described herein, the cell population is contacted or otherwise provided with a candidate (test) differentiation factor. The candidate differentiation factor can comprise any molecule that may have the potential to promote the differentiation of human dorsal and/or ventral PDX1-positive foregut endoderm cells. In some embodiments described herein, the candidate differentiation factor comprises a molecule that is known to be a differentiation factor for one or more types of cells. In alternate embodiments, the candidate differentiation factor comprises a molecule that in not known to promote cell differentiation. In preferred embodiments, the candidate differentiation factor comprises molecule that is not known to promote the differentiation of dorsal and/or ventral PDX1-positive foregut endoderm cells.

In some embodiments of the screening methods described herein, the candidate differentiation factor comprises a small molecule. In preferred embodiments, a small molecule is a molecule having a molecular mass of about 10,000 amu or less. In some embodiments, the small molecule comprises a retinoid. In some embodiments, the small molecule comprises retinoic acid.

In other embodiments described herein, the candidate differentiation factor comprises a polypeptide. The polypeptide can be any polypeptide including, but not limited to, a glycoprotein, a lipoprotein, an extracellular matrix protein, a cytokine, a chemokine, a peptide hormone, an interleukin or a growth factor. Preferred polypeptides include growth factors.

In some embodiments of the screening methods described herein, the candidate differentiation factors comprise one or more growth factors selected from the group consisting of Amphiregulin, B-lymphocyte stimulator, IL-16, Thymopoietin, TRAIL/Apo-2, Pre B cell colony enhancing factor, Endothelial differentiation-related factor 1 (EDF1), Endothelial monocyte activating polypeptide II, Macrophage migration inhibitory factor (MIF), Natural killer cell enhancing factor (NKEFA), Bone mophogenetic protein 2, Bone mophogenetic protein 8 (osteogeneic protein 2), Bone morphogenic protein 6, Bone morphogenic protein 7, Connective tissue growth factor (CTGF), CGI-149 protein (neuroendocrine differentiation factor), Cytokine A3 (macrophage inflammatory protein 1-alpha), Gliablastoma cell differentiation-related protein (GBDR1), Hepatoma-derived growth factor, Neuromedin U-25 precursor, Vascular endothelial growth factor (VEGF), Vascular endothelial growth factor B (VEGF-B), T-cell specific RANTES precursor, thymic dendritic cell-derived factor 1, Transferrin, Interleukin-1 (IL 1), Interleukin-2 (IL 2), Interleukin-3 (IL 3), Interleukin-4 (IL 4), Interleukin-5 (IL 5), Interleukin-6 (IL 6), Interleukin-7 (IL 7), Interleukin-8 (IL 8), Interleukin-9 (IL 9), Interleukin-10 (IL 10), Interleukin-11 (IL 11), Interleukin-12 (IL 12), Interleukin-13 (IL 13), Granulocyte-colony stimulating factor (G-CSF), Granulocyte macrophage colony stimulating factor (GM-CSF), Macrophage colony stimulating factor (M-CSF), Erythropoietin, Thrombopoietin, Vitamin D3, Epidermal growth factor (EGF), Brain-derived neurotrophic factor, Leukemia inhibitory factor, Thyroid hormone, Basic fibroblast growth factor (bFGF), aFGF, FGF-4, FGF-6, Keratinocyte growth factor (KGF), Platelet-derived growth factor (PDGF), Platelet-derived growth factor-BB, beta nerve growth factor, activin A, Transforming growth factor beta 1 (TGF-(31), Interferon-α, Interferon-(3, Interferon-y, Tumor necrosis factor-α, Tumor necrosis factor-(3, Burst promoting activity (BPA), Erythroid promoting activity (EPA), PGE₂, insulin growth factor-1 (IGF-1), IGF-II, Neutrophin growth factor (NGF), Neutrophin-3, Neutrophin 4/5, Ciliary neurotrophic factor, Glial-derived nexin, Dexamethasone, (3-mercaptoethanol, Retinoic acid, Butylated hydroxyanisole, 5-azacytidine, Amphotericin B, Ascorbic acid, Ascrorbate, isobutylxanthine, indomethacin, β-glycerolphosphate, nicotinamide, DMSO, Thiazolidinediones, TWS119, oxytocin, vasopressin, melanocyte-stimulating hormone, corticortropin, lipotropin, thyrotropin, growth hormone, prolactin, luteinizing hormone, human chorionic gonadotropin, follicle stimulating hormone, corticotropin-releasing factor, gonadotropin-releasing factor, prolactin-releasing factor, prolactin-inhibiting factor, growth-hormone releasing factor, somatostatin, thyrotropin-releasing factor, calcitonin gene-related peptide, parathyroid hormone, glucagon-like peptide 1, glucose-dependent insulinotropic polypeptide, gastrin, secretin, cholecystokinin, motilin, vasoactive intestinal peptide, substance P, pancreatic polypeptide, peptide tyrosine tyrosine, neuropeptide tyrosine, insulin, glucagon, placental lactogen, relaxin, angiotensin II, calctriol, atrial natriuretic peptide, and melatonin. thyroxine, triiodothyronine, calcitonin, estradiol, estrone, progesterone, testosterone, cortisol, corticosterone, aldosterone, epinephrine, norepinepherine, androstiene, calcitriol, collagen, Dexamethasone, 0-mercaptoethanol, Retinoic acid, Butylated hydroxyanisole, 5-azacytidine, Amphotericin B, Ascorbic acid, Ascrorbate, isobutylxanthine, indomethacin, 0-glycerolphosphate, nicotinamide, DMSO, Thiazolidinediones, and TWS119.

In some embodiments of the screening methods described herein, the candidate differentiation factor is provided to the cell population in one or more concentrations. In some embodiments, the candidate differentiation factor is provided to the cell population so that the concentration of the candidate differentiation factor in the medium surrounding the cells ranges from about 0.1 ng/ml to about 10 mg/ml. In some embodiments, the concentration of the candidate differentiation factor in the medium surrounding the cells ranges from about 1 ng/ml to about 1 mg/ml. In other embodiments, the concentration of the candidate differentiation factor in the medium surrounding the cells ranges from about 10 ng/ml to about 100 μg/ml. In still other embodiments, the concentration of the candidate differentiation factor in the medium surrounding the cells ranges from about 100 ng/ml to about 10 μg/ml. In preferred embodiments, the concentration of the candidate differentiation factor in the medium surrounding the cells is about 5 ng/ml, about 25 ng/ml, about 50 ng/ml, about 75 ng/ml, about 100 ng/ml, about 125 ng/ml, about 150 ng/ml, about 175 ng/ml, about 200 ng/ml, about 225 ng/ml, about 250 ng/ml, about 275 ng/ml, about 300 ng/ml, about 325 ng/ml, about 350 ng/ml, about 375 ng/ml, about 400 ng/ml, about 425 ng/ml, about 450 ng/ml, about 475 ng/ml, about 500 ng/ml, about 525 ng/ml, about 550 ng/ml, about 575 ng/ml, about 600 ng/ml, about 625 ng/ml, about 650 ng/ml, about 675 ng/ml, about 700 ng/ml, about 725 ng/ml, about 750 ng/ml, about 775 ng/ml, about 800 ng/ml, about 825 ng/ml, about 850 ng/ml, about 875 ng/ml, about 900 ng/ml, about 925 ng/ml, about 950 ng/ml, about 975 ng/ml, about 1 μg/ml, about 2 μg/ml, about 3 μg/ml, about 4 μg/ml, about 5 μg/ml, about 6 μg/ml, about 7 μg/ml, about 8 μg/ml, about 9 μg/ml, about 10 μg/ml, about 11 μg/ml, about 12 μg/ml, about 13 μg/ml, about 14 μg/ml, about 15 μg/ml, about 16 μg/ml, about 17 μg/ml, about 18 μg/ml, about 19 μg/ml, about 20 μg/ml, about 25 μg/ml, about 50 μg/ml, about 75 μg/ml, about 100 μg/ml, about 125 μg/ml, about 150 μg/ml, about 175 μg/ml, about 200 μg/ml, about 250 μg/ml, about 300 μg/ml, about 350 μg/ml, about 400 μg/ml, about 450 μg/ml, about 500 μg/ml, about 550 μg/ml, about 600 μg/ml, about 650 μg/ml, about 700 μg/ml, about 750 μg/ml, about 800 μg/ml, about 850 μg/ml, about 900 μg/ml, about 950 μg/ml, about 1000 μg/ml or greater than about 1000 μg/ml.

In certain embodiments of the screening methods described herein, the cell population is provided with a candidate differentiation factor which comprises any molecule other than a retinoid, FGF-10, FGF-4, BMP-4, activin A, activin B or any other foregut differentiation factor. In some embodiments, the cell population is provided with a candidate differentiation factor which comprises any molecule other than retinoic acid.

In some embodiments, steps of the screening methods described herein comprise determining expression of at least one marker at a first time point and a second time point. In some of these embodiments, the first time point can be prior to or at approximately the same time as providing the cell population with the candidate differentiation factor. Alternatively, in some embodiments, the first time point is subsequent to providing the cell population with the candidate differentiation factor. In some embodiments, expression of a plurality of markers is determined at a first time point.

In addition to determining expression of at least one marker at a first time point, some embodiments of the screening methods described herein contemplate determining expression of at least one marker at a second time point, which is subsequent to the first time point and which is subsequent to providing the cell population with the candidate differentiation factor. In such embodiments, expression of the same marker is determined at both the first and second time points. In some embodiments, expression of a plurality of markers is determined at both the first and second time points. In such embodiments, expression of the same plurality of markers is determined at both the first and second time points. In some embodiments, marker expression is determined at a plurality of time points, each of which is subsequent to the first time point, and each of which is subsequent to providing the cell population with the candidate differentiation factor. In certain embodiments, marker expression is determined by Q-PCR. In other embodiments, marker expression is determined by immunocytochemistry.

In certain embodiments of the screening methods described herein, the marker having its expression is determined at the first and second time points is a marker that is associated with the differentiation of human dorsal and/or ventral PDX1-positive foregut endoderm cells to cells which are the precursors of cells which make up tissues and/or organs that are derived from the posterior portion of the foregut. In some embodiments, the tissues and/or organs that are derived from the posterior portion of the foregut comprise terminally differentiated cells. In some embodiments, the marker is indicative of pancreatic cells or pancreatic precursor cells. In some embodiments, the marker is a marker that is selected from Table 3 or Table 4.

In some embodiments of the screening methods described herein, sufficient time is allowed to pass between providing the cell population with the candidate differentiation factor and determining marker expression at the second time point. Sufficient time between providing the cell population with the candidate differentiation factor and determining expression of the marker at the second time point can be as little as from about 1 hour to as much as about 10 days. In some embodiments, the expression of at least one marker is determined multiple times subsequent to providing the cell population with the candidate differentiation factor. In some embodiments, sufficient time is at least about 1 hour, at least about 6 hours, at least about 12 hours, at least about 18 hours, at least about 24 hours, at least about 30 hours, at least about 36 hours, at least about 42 hours, at least about 48 hours, at least about 54 hours, at least about 60 hours, at least about 66 hours, at least about 72 hours, at least about 78 hours, at least about 84 hours, at least about 90 hours, at least about 96 hours, at least about 102 hours, at least about 108 hours, at least about 114 hours, at least about 120 hours, at least about 126 hours, at least about 132 hours, at least about 138 hours, at least about 144 hours, at least about 150 hours, at least about 156 hours, at least about 162 hours, at least about 168 hours, at least about 174 hours, at least about 180 hours, at least about 186 hours, at least about 192 hours, at least about 198 hours, at least about 204 hours, at least about 210 hours, at least about 216 hours, at least about 222 hours, at least about 228 hours, at least about 234 hours or at least about 240 hours.

In some embodiments of the methods described herein, it is further determined whether the expression of the marker at the second time point has increased or decreased as compared to the expression of this marker at the first time point. An increase or decrease in the expression of the at least one marker indicates that the candidate differentiation factor is capable of promoting the differentiation of the dorsal and/or ventral PDX1-positive foregut endoderm cells. Similarly, if expression of a plurality of markers is determined, it is further determined whether the expression of the plurality of markers at the second time point has increased or decreased as compared to the expression of this plurality of markers at the first time point. An increase or decrease in marker expression can be determined by measuring or otherwise evaluating the amount, level or activity of the marker in the cell population at the first and second time points. Such determination can be relative to other markers, for example housekeeping gene expression, or absolute. In certain embodiments, wherein marker expression is increased at the second time point as compared with the first time point, the amount of increase is at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, at least about 100-fold or more than at least about 100-fold. In some embodiments, the amount of increase is less than 2-fold. In embodiments where marker expression is decreased at the second time point as compared with the first time point, the amount of decrease is at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, at least about 100-fold or more than at least about 100-fold. In some embodiments, the amount of decrease is less than 2-fold.

Although each of the methods disclosed herein have been described with respect to dorsal and/or ventral PDX1-positive foregut endoderm cells, it will be appreciated that in certain embodiments, these methods can be used to produce compositions comprising the dorsal and/or ventral PDX1-positive foregut/midgut endoderm cells that are described herein and/or the dorsal and/or ventral PDX1-positive endoderm cells of the posterior portion of the foregut that are described herein. Furthermore, any of the PDX1-positive endoderm cell types disclosed in this specification can be utilized in the screening methods described herein.

Having generally described this invention, a further understanding can be obtained by reference to certain specific examples which are provided herein for purposes of illustration only, and are not intended to be limiting.

EXAMPLES

Many of the examples below describe the use of pluripotent human cells. Methods of producing pluripotent human cells are well known in the art and have been described numerous scientific publications, including U.S. Pat. Nos. 5,453,357, 5,670,372, 5,690,926, 6,090,622, 6,200,806 and 6,251,671 as well as U.S. Patent Application Publication No. 2004/0229350, the disclosures of which are incorporated herein by reference in their entireties.

Example 1 Human ES Cells

For our studies of endoderm development we employed human embryonic stem cells, which are pluripotent and can divide seemingly indefinitely in culture while maintaining a normal karyotype. ES cells were derived from the 5-day-old embryo inner cell mass using either immunological or mechanical methods for isolation. In particular, the human embryonic stem cell line hESCyt-25 was derived from a supernumerary frozen embryo from an in vitro fertilization cycle following informed consent by the patient. Upon thawing the hatched blastocyst was plated on mouse embryonic fibroblasts (MEF), in ES medium (DMEM, 20% PBS, non essential amino acids, beta-mercaptoethanol, ITS supplement). The embryo adhered to the culture dish and after approximately two weeks, regions of undifferentiated hESCs were transferred to new dishes with MEFs. Transfer was accomplished with mechanical cutting and a brief digestion with dispase, followed by mechanical removal of the cell clusters, washing and re-plating. Since derivation, hESCyt-25 has been serially passaged over 100 times. We employed the hESCyt-25 human embryonic stem cell line as our starting material for the production of definitive endoderm.

It will be appreciated by those of skill in the art that stem cells or other pluripotent cells can also be used as starting material for the differentiation procedures described herein. For example, cells obtained from embryonic gonadal ridges, which can be isolated by methods known in the art, can be used as pluripotent cellular starting material.

Example 2

hESCyt-25 Characterization

The human embryonic stem cell line, hESCyt-25 has maintained a normal morphology, karyotype, growth and self-renewal properties over 18 months in culture. This cell line displays strong immunoreactivity for the OCT4, SSEA-4 and TRA-1-60 antigens, all of which, are characteristic of undifferentiated hESCs and displays alkaline phosphatase activity as well as a morphology identical to other established hESC lines. Furthermore, the human stem cell line, hESCyt-25, also readily forms embryoid bodies (EBs) when cultured in suspension. As a demonstration of its pluripotent nature, hESCyT-25 differentiates into various cell types that represent the three principal germ layers. Ectoderm production was demonstrated by Q-PCR for ZIC1 as well as immunocytochemistry (ICC) for nestin and more mature neuronal markers. Immunocytochemical staining for 13-111 tubulin was observed in clusters of elongated cells, characteristic of early neurons. Previously, we treated EBs in suspension with retinoic acid, to induce differentiation of pluripotent stem cells to visceral endoderm (VE), an extra-embryonic lineage. Treated cells expressed high levels of oc-fetoprotein (AFP) and SOX7, two markers of VE, by 54 hours of treatment. Cells differentiated in monolayer expressed AFP in sporadic patches as demonstrated by immunocytochemical staining. As will be described below, the hESCyT-25 cell line was also capable of forming definitive endoderm, as validated by real-time quantitative polymerase chain reaction (Q-PCR) and immunocytochemistry for SOX17, in the absence of AFP expression. To demonstrate differentiation to mesoderm, differentiating EBs were analyzed for Brachyury gene expression at several time points. Brachyury expression increased progressively over the course of the experiment. In view of the foregoing, the hESCyT-25 line is pluripotent as shown by the ability to form cells representing the three germ layers.

Example 3 Production of S OX17 Antibody

A primary obstacle to the identification of definitive endoderm in hESC cultures is the lack of appropriate tools. We therefore undertook the production of an antibody raised against human SOX17 protein.

The marker SOX17 is expressed throughout the definitive endoderm as it forms during gastrulation and its expression is maintained in the gut tube (although levels of expression vary along the A-P axis) until around the onset of organogenesis. SOX17 is also expressed in a subset of extra-embryonic endoderm cells. No expression of this protein has been observed in mesoderm or ectoderm. It has now been discovered that SOX17 is an appropriate marker for the definitive endoderm lineage when used in conjunction with markers to exclude extra-embryonic lineages.

As described in detail herein, the SOX17 antibody was utilized to specifically examine effects of various treatments and differentiation procedures aimed at the production of SOX17 positive definitive endoderm cells. Other antibodies reactive to AFP, SPARC and Thrombomodulin were also employed to rule out the production of visceral and parietal endoderm (extra-embryonic endoderm).

In order to produce an antibody against SOX17, a portion of the human SOX17 cDNA (SEQ ID NO: 1) corresponding to amino acids 172-414 (SEQ ID NO: 2) in the carboxyterminal end of the SOX17 protein (FIG. 2 ) was used for genetic immunization in rats at the antibody production company, GENOVAC (Freiberg, Germany), according to procedures developed there. Procedures for genetic immunization can be found in U.S. Pat. Nos. 5,830,876, 5,817,637, 6,165,993 and 6,261,281 as well as International Patent Application Publication Nos. WO00/29442 and WO99/13915, the disclosures of which are incorporated herein by reference in their entireties.

Other suitable methods for genetic immunization are also described in the non-patent literature. For example, Barry et al. describe the production of monoclonal antibodies by genetic immunization in Biotechniques 16: 616-620, 1994, the disclosure of which is incorporated herein by reference in its entirety. Specific examples of genetic immunization methods to produce antibodies against specific proteins can be found, for example, in Costaglia et al., (1998) Genetic immunization against the human thyrotropin receptor causes thyroiditis and allows production of monoclonal antibodies recognizing the native receptor, J. Immunol. 160: 1458-1465; Kilpatrick et al (1998) Gene gun delivered DNA-based immunizations mediate rapid production of murine monoclonal antibodies to the Flt-3 receptor, Hybridoma 17: 569-576; Schmolke et al., (1998) Identification of hepatitis G virus particles in human serum by E2-specific monoclonal antibodies generated by DNA immunization, J. Virol. 72: 4541-4545; Krasemann et al., (1999) Generation of monoclonal antibodies against proteins with an unconventional nucleic acid-based immunization strategy, J. Biotechnol. 73: 119-129; and Ulivieri et al., (1996) Generation of a monoclonal antibody to a defined portion of the Heliobacter pylori vacuolating cytotoxin by DNA immunization, J. Biotechnol. 51: 191-194, the disclosures of which are incorporated herein by reference in their entireties.

SOX7 and SOX18 are the closest Sox family relatives to SOX17 as depicted in the relational dendrogram shown in FIG. 3 . We employed the human SOX7 polypeptide as a negative control to demonstrate that the SOX17 antibody produced by genetic immunization is specific for SOX17 and does not react with its closest family member. In particular, SOX7 and other proteins were expressed in human fibroblasts, and then, analyzed for cross reactivity with the SOX17 antibody by Western blot and ICC. For example, the following methods were utilized for the production of the SOX17, SOX7 and EGFP expression vectors, their transfection into human fibroblasts and analysis by Western blot. Expression vectors employed for the production of SOX17, SOX7, and EGFP were pCMV6 (OriGene Technologies, Inc., Rockville, MD), pCMV-SPORT6 (Invitrogen, Carlsbad, Calif.) and pEGFP-N1 (Clonetech, Palo Alto, Calif.), respectively. For protein production, telomerase immortalized MDX human fibroblasts were transiently transfected with supercoiled DNA in the presence of Lipofectamine 2000 (Invitrogen, Carlsbad, Calif.). Total cellular lysates were collected 36 hours post-transfection in 50 mM TRIS-HCl (pH 8), 150 mM NaCl, 0.1% SDS, 0.5% deoxycholate, containing a cocktail of protease inhibitors (Roche Diagnostics Corporation, Indianapolis, IN). Western blot analysis of 100 μg of cellular proteins, separated by SDS-PAGE on NuPAGE (4-12% gradient polyacrylamide, Invitrogen, Carlsbad, Calif.), and transferred by electro-blotting onto PDVF membranes (Hercules, Calif.), were probed with a 1/1000 dilution of the rat SOX17 anti-serum in 10 mM TRIS-HCl (pH 8), 150 mM NaCl, 10% BSA, 0.05% Tween-20 (Sigma, St. Louis, MO), followed by Alkaline Phosphatase conjugated anti-rat IgG (Jackson ImmunoResearch Laboratories, West Grove, Pa.), and revealed through Vector Black Alkaline Phosphatase staining (Vector Laboratories, Burlingame, Calif.). The proteins size standard used was wide range color markers (Sigma, St. Louis, Mo.).

In FIG. 4 , protein extracts made from human fibroblast cells that were transiently transfected with SOX17, SOX7 or EGFP cDNA's were probed on Western blots with the SOX17 antibody. Only the protein extract from hSOX17 transfected cells produced a band of ˜51Kda which closely matched the predicted 46 Kda molecular weight of the human SOX17 protein. There was no reactivity of the SOX17 antibody to extracts made from either human SOX7 or EGFP transfected cells. Furthermore, the SOX17 antibody clearly labeled the nuclei of human fibroblast cells transfected with the hSOX17 expression construct but did not label cells transfected with EGFP alone. As such, the SOX17 antibody exhibits specificity by ICC.

Example 4 Validation of SOX17 Antibody as a Marker of Definitive Endoderm

Partially differentiated hESCs were co-labeled with SOX17 and AFP antibodies to demonstrate that the SOX17 antibody is specific for human SOX17 protein and furthermore marks definitive endoderm. It has been demonstrated that SOX17, SOX7 (which is a closely related member of the SOX gene family subgroup F (FIG. 3 )) and AFP are each expressed in visceral endoderm. However, AFP and SOX7 are not expressed in definitive endoderm cells at levels detectable by ICC, and thus, they can be employed as negative markers for bonifide definitive endoderm cells. It was shown that SOX17 antibody labels populations of cells that exist as discrete groupings of cells or are intermingled with AFP positive cells. In particular, FIG. 5A shows that small numbers of SOX17 cells were co-labeled with AFP; however, regions were also found where there were little or no AFP cells in the field of SOX17+cells (FIG. 5B). Similarly, since parietal endoderm has been reported to express SOX17, antibody co-labeling with SOX17 together with the parietal markers SPARC and/or Thrombomodulin (TM) can be used to identify the SOX17⁺ cells that are parietal endoderm. As shown in FIGS. 6A-C, Thrombomodulin and SOX17 co-labeled parietal endoderm cells were produced by random differentiation of hES cells.

In view of the above cell labeling experiments, the identity of a definitive endoderm cell can be established by the marker profile SOX17¹⁷/AFP^(lo)/[TM^(lo) or SPARC^(lo)]. In other words, the expression of the SOX17 marker is greater than the expression of the AFP marker, which is characteristic of visceral endoderm, and the TM or SPARC markers, which are characteristic of parietal endoderm. Accordingly, those cells positive for SOX17 but negative for AFP and negative for TM or SPARC are definitive endoderm.

As a further evidence of the specificity of the SOX17^(hi)/AFP^(lo)/TM^(lo)/SPARC^(lo) marker profile as predictive of definitive endoderm, SOX17 and AFP gene expression was quantitatively compared to the relative number of antibody labeled cells. As shown in FIG. 7A, hESCs treated with retinoic acid (visceral endoderm inducer), or activin A (definitive endoderm inducer), resulted in a 10-fold difference in the level of SOX17 mRNA expression. This result mirrored the 10-fold difference in SOX17 antibody-labeled cell number (FIG. 7B). Furthermore, as shown in FIG. 8A, activin A treatment of hESCs suppressed AFP gene expression by 6.8-fold in comparison to no treatment. This was visually reflected by a dramatic decrease in the number of AFP labeled cells in these cultures as shown in FIGS. 8B-C. To quantify this further, it was demonstrated that this approximately 7-fold decrease in AFP gene expression was the result of a similar 7-fold decrease in AFP antibody-labeled cell number as measured by flow cytometry (FIGS. 9A-B). This result is extremely significant in that it indicates that quantitative changes in gene expression as seen by Q-PCR mirror changes in cell type specification as observed by antibody staining.

Incubation of hESCs in the presence of Nodal family members (Nodal, activin A and activin B—NAA) resulted in a significant increase in SOX17 antibody-labeled cells over time. By 5 days of continuous activin treatment greater than 50% of the cells were labeled with SOX17 (FIGS. 10A-F). There were few or no cells labeled with AFP after 5 days of activin treatment.

In summary, the antibody produced against the carboxy-terminal 242 amino acids of the human SOX17 protein identified human SOX17 protein on Western blots but did not recognize SOX7, it's closest Sox family relative. The SOX17 antibody recognized a subset of cells in differentiating hESC cultures that were primarily SOX17⁺/AFP^(lo/−) (greater than 95% of labeled cells) as well as a small percentage (<5%) of cells that co-label for SOX17 and AFP (visceral endoderm). Treatment of hESC cultures with activins resulted in a marked elevation of SOX17 gene expression as well as SOX17 labeled cells and dramatically suppressed the expression of AFP mRNA and the number of cells labeled with AFP antibody.

Example 5 Q-PCR Gene Expression Assay

In the following experiments, real-time quantitative RT-PCR (Q-PCR) was the primary assay used for screening the effects of various treatments on hESC differentiation. In particular, real-time measurements of gene expression were analyzed for multiple marker genes at multiple time points by Q-PCR. Marker genes characteristic of the desired as well as undesired cell types were evaluated to gain a better understanding of the overall dynamics of the cellular populations. The strength of Q-PCR analysis includes its extreme sensitivity and relative ease of developing the necessary markers, as the genome sequence is readily available. Furthermore, the extremely high sensitivity of Q-PCR permits detection of gene expression from a relatively small number of cells within a much larger population. In addition, the ability to detect very low levels of gene expression provides indications for “differentiation bias” within the population. The bias towards a particular differentiation pathway, prior to the overt differentiation of those cellular phenotypes, is unrecognizable using immunocytochemical techniques. For this reason, Q-PCR provides a method of analysis that is at least complementary and potentially much superior to immunocytochemical techniques for screening the success of differentiation treatments. Additionally, Q-PCR provides a mechanism by which to evaluate the success of a differentiation protocol in a quantitative format at semi-high throughput scales of analysis.

The approach taken here was to perform relative quantitation using SYBR Green chemistry on a Rotor Gene 3000 instrument (Corbett Research) and a two-step RT-PCR format. Such an approach allowed for the banking of cDNA samples for analysis of additional marker genes in the future, thus avoiding variability in the reverse transcription efficiency between samples.

Primers were designed to lie over exon-exon boundaries or span introns of at least 800 bp when possible, as this has been empirically determined to eliminate amplification from contaminating genomic DNA. When marker genes were employed that do not contain introns or they possess pseudogenes, DNase I treatment of RNA samples was performed.

We routinely used Q-PCR to measure the gene expression of multiple markers of target and non-target cell types in order to provide a broad profile description of gene expression in cell samples. The markers relevant for the early phases of hESC differentiation (specifically ectoderm, mesoderm, definitive endoderm and extra-embryonic endoderm) and for which validated primer sets are available are provided below in Table 1. The human specificity of these primer sets has also been demonstrated. This is an important fact since the hESCs were often grown on mouse feeder layers. Most typically, triplicate samples were taken for each condition and independently analyzed in duplicate to assess the biological variability associated with each quantitative determination.

To generate PCR template, total RNA was isolated using RNeasy (Qiagen) and quantitated using RiboGreen (Molecular Probes). Reverse transcription from 350-500 ng of total RNA was carried out using the iScript reverse transcriptase kit (BioRad), which contains a mix of oligo-dT and random primers. Each 20 μL reaction was subsequently diluted up to 100 μL total volume and 3 μL was used in each 10 μL Q-PCR reaction containing 400 nM forward and reverse primers and 5 μL 2X SYBR Green master mix (Qiagen). Two step cycling parameters were used employing a 5 second denature at 85-94° C. (specifically selected according to the melting temp of the amplicon for each primer set) followed by a 45 second anneal/extend at 60° C. Fluorescence data was collected during the last 15 seconds of each extension phase. A three point, 10-fold dilution series was used to generate the standard curve for each run and cycle thresholds (Ct's) were converted to quantitative values based on this standard curve. The quantitated values for each sample were normalized to housekeeping gene performance and then average and standard deviations were calculated for triplicate samples. At the conclusion of PCR cycling, a melt curve analysis was performed to ascertain the specificity of the reaction. A single specific product was indicated by a single peak at the Tm appropriate for that PCR amplicon. In addition, reactions performed without reverse transcriptase served as the negative control and do not amplify.

A first step in establishing the Q-PCR methodology was validation of appropriate housekeeping genes (HGs) in the experimental system. Since the HG was used to normalize across samples for the RNA input, RNA integrity and RT efficiency, it was of value that the HG exhibited a constant level of expression over time in all sample types in order for the normalization to be meaningful. We measured the expression levels of Cyclophilin G, hypoxanthine phosphoribosyltransferase 1 (HPRT), beta-2-microglobulin, hydroxymethylbiane synthase (HMBS), TATA-binding protein (TBP), and glucoronidase beta (GUS) in differentiating hESCs. Our results indicated that beta-2-microglobulin expression levels increased over the course of differentiation and therefore we excluded the use of this gene for normalization. The other genes exhibited consistent expression levels over time as well as across treatments. We routinely used both Cyclophilin G and GUS to calculate a normalization factor for all samples. The use of multiple HGs simultaneously reduces the variability inherent to the normalization process and increases the reliability of the relative gene expression values.

After obtaining genes for use in normalization, Q-PCR was then utilized to determine the relative gene expression levels of many marker genes across samples receiving different experimental treatments. The marker genes employed have been chosen because they exhibit enrichment in specific populations representative of the early germ layers and in particular have focused on sets of genes that are differentially expressed in definitive endoderm and extra-embryonic endoderm. These genes as well as their relative enrichment profiles are highlighted in Table 1.

TABLE 1 Germ Layer Gene Expression Domains Endoderm SOX17 definitive, visceral and parietal endoderm MIXL1 endoderm and mesoderm GATA4 definitive and primitive endoderm HNF3b definitive endoderm and primitive endoderm, mesoderm, neural plate GSC endoderm and mesoderm Extra- SOX7 visceral endoderm embryonic AFP visceral endoderm, liver SPARC parietal endoderm TM parietal endoderm/trophectoderm Ectoderm ZIC1 neural tube, neural progenitors Mesoderm BRACH nascent mesoderm

Since many genes are expressed in more than one germ layer it is useful to quantitatively compare expression levels of many genes within the same experiment. SOX17 is expressed in definitive endoderm and to a smaller extent in visceral and parietal endoderm. SOX7 and AFP are expressed in visceral endoderm at this early developmental time point. SPARC and TM are expressed in parietal endoderm and Brachyury is expressed in early mesoderm.

Definitive endoderm cells were predicted to express high levels of SOX17 mRNA and low levels of AFP and SOX7 (visceral endoderm), SPARC (parietal endoderm) and Brachyury (mesoderm). In addition, ZIC1 was used here to further rule out induction of early ectoderm. Finally, GATA4 and HNF3b were expressed in both definitive and extra-embryonic endoderm, and thus, correlate with SOX17 expression in definitive endoderm (Table 1). A representative experiment is shown in FIGS. 11-14 which demonstrates how the marker genes described in Table 1 correlate with each other among the various samples, thus highlighting specific patterns of differentiation to definitive endoderm and extra-embryonic endoderm as well as to mesodermal and neural cell types.

In view of the above data it is clear that increasing doses of activin resulted in increasing SOX17 gene expression. Further this SOX17 expression predominantly represented definitive endoderm as opposed to extra-embryonic endoderm. This conclusion stems from the observation that SOX17 gene expression was inversely correlated with AFP, SOX7, and SPARC gene expression.

Example 6 Directed Differentiation of Human ES Cells to Definitive Endoderm

Human ES cell cultures randomly differentiate if cultured under conditions that do not actively maintain their undifferentiated state. This heterogeneous differentiation results in production of extra-embryonic endoderm cells comprised of both parietal and visceral endoderm (AFP, SPARC and SOX7 expression) as well as early ectodermal and mesodermal derivatives as marked by ZIC1 and Nestin (ectoderm) and Brachyury (mesoderm) expression. Definitive endoderm cell appearance has not been examined or specified for lack of specific antibody markers in ES cell cultures. As such, and by default, early definitive endoderm production in ES cell cultures has not been well studied. Since satisfactory antibody reagents for definitive endoderm cells have been unavailable, most of the characterization has focused on ectoderm and extra-embryonic endoderm. Overall, there are significantly greater numbers of extra-embryonic and neurectodermal cell types in comparison to SOX17^(h)′ definitive endoderm cells in randomly differentiated ES cell cultures.

As undifferentiated hESC colonies expand on a bed of fibroblast feeders, the cells at the edges of the colony take on alternative morphologies that are distinct from those cells residing within the interior of the colony. Many of these outer edge cells can be distinguished by their less uniform, larger cell body morphology and by the expression of higher levels of OCT4. It has been described that as ES cells begin to differentiate they alter the levels of OCT4 expression up or down relative to undifferentiated ES cells. Alteration of OCT4 levels above or below the undifferentiated threshold may signify the initial stages of differentiation away from the pluripotent state.

When undifferentiated colonies were examined by SOX17 immunocytochemistry, occasionally small 10-15-cell clusters of SOX17-positive cells were detected at random locations on the periphery and at the junctions between undifferentiated hESC colonies. As noted above, these scattered pockets of outer colony edges appeared to be some of the first cells to differentiate away from the classical ES cell morphology as the colony expanded in size and became more crowded. Younger, smaller fully undifferentiated colonies (<1mm; 4-5 days old) showed no SOX17 positive cells within or at the edges of the colonies while older, larger colonies (1-2 mm diameter, >5days old) had sporadic isolated patches of SOX17 positive, AFP negative cells at the periphery of some colonies or in regions interior to the edge that did not display the classical hESC morphology described previously. Given that this was the first development of an effective SOX17 antibody, definitive endoderm cells generated in such early “undifferentiated” ES cell cultures have never been previously demonstrated.

Based on negative correlations of SOX17 and SPARC gene expression levels by Q-PCR, the vast majority of these SOX17 positive, AFP negative cells will be negative for parietal endoderm markers by antibody co-labeling. This was specifically demonstrated for TM-expressing parietal endoderm cells as shown in FIGS. 15A-B. Exposure to Nodal factors activin A and B resulted in a dramatic decrease in the intensity of TM expression and the number of TM positive cells. By triple labeling using SOX17, AFP and TM antibodies on an activin treated culture, clusters of SOX17 positive cells that were also negative for AFP and TM were observed (FIGS. 16A-D). These are the first cellular demonstrations of SOX17 positive definitive endoderm cells in differentiating hESC cultures (FIGS. 16A-D and 17).

With the SOX17 antibody and Q-PCR tools described above we have explored a number of procedures capable of efficiently programming hESCs to become SOX17^(hi)/AFP^(lo)/SPARC/TM^(lo) definitive endoderm cells. We applied a variety of differentiation protocols aimed at increasing the number and proliferative capacity of these cells as measured at the population level by Q-PCR for SOX17 gene expression and at the level of individual cells by antibody labeling of SOX17 protein.

We were the first to analyze and describe the effect of TGFβ family growth factors, such as Nodal/activin/BMP, for use in creating definitive endoderm cells from embryonic stem cells in in vitro cell cultures. In typical experiments, activin A, activin B, BMP or combinations of these growth factors were added to cultures of undifferentiated human stem cell line hESCyt-25 to begin the differentiation process.

As shown in FIG. 19 , addition of activin A at 100 ng/ml resulted in a 19-fold induction of SOX17 gene expression vs. undifferentiated hESCs by day 4 of differentiation. Adding activin B, a second member of the activin family, together with activin A, resulted in a 37-fold induction over undifferentiated hESCs by day 4 of combined activin treatment. Finally, adding a third member of the TGFβ family from the Nodal/Activin and BMP subgroups, BMP4, together with activin A and activin B, increased the fold induction to 57 times that of undifferentiated hESCs (FIG. 19 ). When SOX17 induction with activins and BMP was compared to no factor medium controls 5-, 10-, and 15-fold inductions resulted at the 4-day time point. By five days of triple treatment with activins A, B and BMP, SOX17 was induced more than 70 times higher than hESCs. These data indicate that higher doses and longer treatment times of the Nodal/activin TGFβ family members results in increased expression of SOX17.

Nodal and related molecules activin A, B and BMP facilitate the expression of SOX17 and definitive endoderm formation in vivo or in vitro. Furthermore, addition of BMP results in an improved SOX17 induction possibly through the further induction of Cripto, the Nodal co-receptor.

We have demonstrated that the combination of activins A and B together with BMP4 result in additive increases in SOX17 induction and hence definitive endoderm formation. BMP4 addition for prolonged periods (>4 days), in combination with activin A and B may induce SOX17 in parietal and visceral endoderm as well as definitive endoderm. In some embodiments of the present invention, it is therefore valuable to remove BMP4 from the treatment within 4 days of addition.

To determine the effect of TGFβ factor treatment at the individual cell level, a time course of TGFβ factor addition was examined using SOX17 antibody labeling. As previously shown in FIGS. 10A-F, there was a dramatic increase in the relative number of SOX17 labeled cells over time. The relative quantification (FIG. 20 ) shows more than a 20-fold increase in SOX17-labeled cells. This result indicates that both the numbers of cells as well SOX17 gene expression level are increasing with time of TGFβ factor exposure. As shown in FIG. 21 , after four days of exposure to Nodal, activin A, activin B and BMP4, the level of SOX17 induction reached 168-fold over undifferentiated hESCs. FIG. 22 shows that the relative number of SOX17-positive cells was also dose responsive. activin A doses of 100 ng/ml or more were capable of potently inducing SOX17 gene expression and cell number.

In addition to the TGFβ family members, the Wnt family of molecules may play a role in specification and/or maintenance of definitive endoderm. The use of Wnt molecules was also beneficial for the differentiation of hESCs to definitive endoderm as indicated by the increased SOX17 gene expression in samples that were treated with activins plus Wnt3a over that of activins alone (FIG. 23 ).

All of the experiments described above were performed using a tissue culture medium containing 10% serum with added factors. Surprisingly, we discovered that the concentration of serum had an effect on the level of SOX17 expression in the presence of added activins as shown in FIGS. 24A-C. When serum levels were reduced from 10% to 2%, SOX17 expression tripled in the presence of activins A and B.

Finally, we demonstrated that activin induced SOX17⁺ cells divide in culture as depicted in FIGS. 25A-D. The arrows show cells labeled with SOX17/PCNA/DAPI that are in mitosis as evidenced by the PCNA/DAPI-labeled mitotic plate pattern and the phase contrast mitotic profile.

Example 7

Chemokine Receptor 4 (CXCR4) Expression Correlates with Markers for Definitive Endoderm and not Markers for Mesoderm, Ectoderm or Visceral Endoderm

As described above, hESCs can be induced to differentiate to the definitive endoderm germ layer by the application of cytokines of the TGFβ family and more specifically of the activin/nodal subfamily Additionally, we have shown that the proportion of fetal bovine serum (FBS) in the differentiation culture medium effects the efficiency of definitive endoderm differentiation from hESCs. This effect is such that at a given concentration of activin A in the medium, higher levels of FBS will inhibit maximal differentiation to definitive endoderm. In the absence of exogenous activin A, differentiation of hESCs to the definitive endoderm lineage is very inefficient and the FBS concentration has much milder effects on the differentiation process of hESCs.

In these experiments, hESCs were differentiated by growing in RPMI medium (Invitrogen, Carlsbad, CA; cat# 61870-036) supplemented with 0.5%, 2.0% or 10% FBS and either with or without 100 ng/ml activin A for 6 days. In addition, a gradient of FBS ranging from 0.5% to 2.0% over the first three days of differentiation was also used in conjunction with 100 ng/ml of activin A. After the 6 days, replicate samples were collected from each culture condition and analyzed for relative gene expression by real-time quantitative PCR. The remaining cells were fixed for immunofluorescent detection of SOX17 protein.

The expression levels of CXCR4 varied dramatically across the 7 culture conditions used (FIG. 26 ). In general, CXCR4 expression was high in activin A treated cultures (A100) and low in those which did not receive exogenous activin A (NF). In addition, among the A100 treated cultures, CXCR4 expression was highest when FBS concentration was lowest. There was a remarkable decrease in CXCR4 level in the 10% FBS condition such that the relative expression was more in line with the conditions that did not receive activin A (NF).

As described above, expression of the SOX17, GSC, MIXL1, and HNF313 genes is consistent with the characterization of a cell as definitive endoderm. The relative expression of these four genes across the 7 differentiation conditions mirrors that of CXCR4 (FIGS. 27A-D). This demonstrates that CXCR4 is also a marker of definitive endoderm.

Ectoderm and mesoderm lineages can be distinguished from definitive endoderm by their expression of various markers. Early mesoderm expresses the genes Brachyury and MOX1 while nascent neuro-ectoderm expresses SOX1 and ZIC1. FIGS. 28A-D demonstrate that the cultures which did not receive exogenous activin A were preferentially enriched for mesoderm and ectoderm gene expression and that among the activin A treated cultures, the 10% FBS condition also had increased levels of mesoderm and ectoderm marker expression. These patterns of expression were inverse to that of CXCR4 and indicated that CXCR4 was not highly expressed in mesoderm or ectoderm derived from hESCs at this developmental time period.

Early during mammalian development, differentiation to extra-embryonic lineages also occurs. Of particular relevance here is the differentiation of visceral endoderm that shares the expression of many genes in common with definitive endoderm, including SOX17. To distinguish definitive endoderm from extra-embryonic visceral endoderm one should examine a marker that is distinct between these two. SOX7 represents a marker that is expressed in the visceral endoderm but not in the definitive endoderm lineage. Thus, culture conditions that exhibit robust SOX17 gene expression in the absence of SOX7 expression are likely to contain definitive and not visceral endoderm. It is shown in FIG. 28E that SOX7 was highly expressed in cultures that did not receive activin A, SOX7 also exhibited increased expression even in the presence of activin A when FBS was included at 10%. This pattern is the inverse of the CXCR4 expression pattern and suggests that CXCR4 is not highly expressed in visceral endoderm.

The relative number of SOX17 immunoreactive (SOX17±) cells present in each of the differentiation conditions mentioned above was also determined. When hESCs were differentiated in the presence of high dose activin A and low FBS concentration (0.5%-2.0%) SOX17⁺ cells were ubiquitously distributed throughout the culture. When high dose activin A was used but FBS was included at 10% (v/v), the SOX17⁺ cells appeared at much lower frequency and always appeared in isolated clusters rather than evenly distributed throughout the culture (FIGS. 29A and C as well as B and E). A further decrease in SOX17⁺ cells was seen when no exogenous activin A was used. Under these conditions the SOX17⁺ cells also appeared in clusters and these clusters were smaller and much more rare than those found in the high activin A, low PBS treatment (FIG. 29 C and F). These results demonstrate that the CXCR4 expression patterns not only correspond to definitive endoderm gene expression but also to the number of definitive endoderm cells in each condition.

Example 8

Differentiation Conditions that Enrich for Definitive Endoderm Increase the Proportion of CXCR4 Positive Cells

The dose of activin A also effects the efficiency at which definitive endoderm can be derived from hESCs. This example demonstrates that increasing the dose of activin A increases the proportion of CXCR4⁺ cells in the culture.

hESCs were differentiated in RPMI media supplemented with 0.5%-2% FBS (increased from 0.5% to 1.0% to 2.0% over the first 3 days of differentiation) and either 0, 10, or 100 ng/ml of activin A. After 7 days of differentiation the cells were dissociated in PBS without Ca²⁺/Mg²⁺ containing 2% FBS and 2 mM (EDTA) for 5 minutes at room temperature. The cells were filtered through 35 _(i)ttm nylon filters, counted and pelleted. Pellets were resuspended in a small volume of 50% human serum/50% normal donkey serum and incubated for 2 minutes on ice to block non-specific antibody binding sites. To this, 1 μl of mouse anti-CXCR4 antibody (Abcam, cat# ab10403-100) was added per 50 _(j)ai (containing approximately 10⁵ cells) and labeling proceeded for 45 minutes on ice. Cells were washed by adding 5 ml of PBS containing 2% human serum (buffer) and pelleted. A second wash with 5 ml of buffer was completed then cells were resuspended in 50 _(j)ai buffer per 10⁵ cells. Secondary antibody (FITC conjugated donkey anti-mouse; Jackson ImmunoResearch, cat# 715-096-151) was added at 5 μg/ml final concentration and allowed to label for 30 minutes followed by two washes in buffer as above. Cells were resuspended at 5×10⁶ cells/ml in buffer and analyzed and sorted using a FACS Vantage (Beckton Dickenson) by the staff at the flow cytometry core facility (The Scripps Research Institute). Cells were collected directly into RLT lysis buffer (Qiagen) for subsequent isolation of total RNA for gene expression analysis by real-time quantitative PCR.

The number of CXCR4⁺ cells as determined by flow cytometry were observed to increase dramatically as the dose of activin A was increased in the differentiation culture media (FIGS. 30A-C). The CXCR4⁺ cells were those falling within the R4 gate and this gate was set using a secondary antibody-only control for which 0.2% of events were located in the R4 gate. The dramatically increased numbers of CXCR4⁺ cells correlates with a robust increase in definitive endoderm gene expression as activin A dose is increased (FIGS. 31A-D).

Example 9 Isolation of CXCR4 Positive Cells Enriches for Definitive Endoderm Gene Expression and Depletes Cells Expressing Markers of Mesoderm, Ectoderm and Visceral Endoderm

The CXCR4⁺ and CXCR4⁻cells identified in Example 8 above were collected and analyzed for relative gene expression and the gene expression of the parent populations was determined simultaneously.

The relative levels of CXCR4 gene expression was dramatically increased with increasing dose of activin A (FIG. 32 ). This correlated very well with the activin A dose-dependent increase of CXCR4⁺ cells (FIGS. 30A-C). It is also clear that isolation of the CXCR4⁺ cells from each population accounted for nearly all of the CXCR4 gene expression in that population. This demonstrates the efficiency of the FACS method for collecting these cells.

Gene expression analysis revealed that the CXCR4⁺ cells contain not only the majority of the CXCR4 gene expression, but they also contained gene expression for other markers of definitive endoderm. As shown in FIGS. 31A-D, the CXCR4⁺ cells were further enriched over the parent A100 population for SOX17, GSC, HNF3B, and MIXL I. In addition, the CXCR4⁻fraction contained very little gene expression for these definitive endoderm markers. Moreover, the CXCR4⁺ and CXCR4⁻populations displayed the inverse pattern of gene expression for markers of mesoderm, ectoderm and extra-embryonic endoderm. FIGS. 33A-D shows that the CXCR4⁺ cells were depleted for gene expression of Brachyury, MOX1, ZIC1, and SOX7 relative to the A100 parent population. This A100 parent population was already low in expression of these markers relative to the low dose or no activin A conditions. These results show that the isolation of CXCR4⁺ cells from hESCs differentiated in the presence of high activin A yields a population that is highly enriched for and substantially pure definitive endoderm.

Example 10 Quantitation of Definitive Endoderm Cells in a Cell Population Using CXCR4

To confirm the quantitation of the proportion of definitive endoderm cells present in a cell culture or cell population as determined previously herein and as determined in U.S. Provisional Patent Application No. 60/532,004, entitled DEFINITIVE ENDODERM, filed Dec. 23, 2003, the disclosure of which is incorporated herein by reference in its entirety, cells expressing CXCR4 and other markers of definitive endoderm were analyzed by FACS.

Using the methods such as those described in the above Examples, hESCs were differentiated to produce definitive endoderm. In particular, to increase the yield and purity in differentiating cell cultures, the serum concentration of the medium was controlled as follows: 0.2% FBS on dayl, 1.0% FBS on day 2 and 2.0% FBS on days 3-6. Differentiated cultures were sorted by FACS using three cell surface epitopes, E-Cadherin, CXCR4, and Thrombomodulin. Sorted cell populations were then analyzed by Q-PCR to determine relative expression levels of markers for definitive and extraembryonic-endoderm as well as other cell types. CXCR4 sorted cells taken from optimally differentiated cultures resulted in the isolation of definitive endoderm cells that were >98% pure.

Table 2 shows the results of a marker analysis for a definitive endoderm culture that was differentiated from hESCs using the methods described herein.

TABLE 2 Composition of Definitive Endoderm Cultures Percent Percent Percent Percent of Definitive Extraembryonic hES Marker(s) culture Endoderm endoderm cells SOX17 70-80 100 Thrombomodulin <2 0 75 AFP <1 0 25 CXCR4 70-80 100 0 ECAD 10 0 100 other (ECAD neg.) 10-20 Total 100  100 100 100

In particular, Table 2 indicates that CXCR4 and SOX17 positive cells (endoderm) comprised from 70%-80% of the cells in the cell culture. Of these SOX17-expressing cells, less than 2% expressed TM (parietal endoderm) and less than 1% expressed AFP (visceral endoderm). After subtracting the proportion of TM-positive and AFP-positive cells (combined parietal and visceral endoderm; 3% total) from the proportion of SOX17/CXCR4 positive cells, it can be seen that about 67% to about 77% of the cell culture was definitive endoderm. Approximately 10% of the cells were positive for E-Cadherin (ECAD), which is a marker for hESCs, and about 10-20% of the cells were of other cell types.

We have discovered that the purity of definitive endoderm in the differentiating cell cultures that are obtained prior to FACS separation can be improved as compared to the above-described low serum procedure by maintaining the FBS concentration at ≤0.5% throughout the 5-6 day differentiation procedure. However, maintaining the cell culture at ≤0.5% throughout the 5-6 day differentiation procedure also results in a reduced number of total definitive endoderm cells that are produced.

Definitive endoderm cells produced by methods described herein have been maintained and expanded in culture in the presence of activin for greater than 50 days without appreciable differentiation. In such cases, SOX17, CXCR4, MIXL1, GATA4, HNF313 expression is maintained over the culture period. Additionally, TM, SPARC, OCT4, AFP, SOX7, ZIC1 and BRACH were not detected in these cultures. It is likely that such cells can be maintained and expanded in culture for substantially longer than 50 days without appreciable differentiation.

Example 11 Additional Marker of Definitive Endoderm Cells

In the following experiment, RNA was isolated from purified definitive endoderm and human embryonic stem cell populations. Gene expression was then analyzed by gene chip analysis of the RNA from each purified population. Q-PCR was also performed to further investigate the potential of genes expressed in definitive endoderm, but not in embryonic stem cells, as a marker for definitive endoderm.

Human embryonic stem cells (hESCs) were maintained in DMEM/F12 media supplemented with 20% KnockOut Serum Replacement, 4 ng/ml recombinant human basic fibroblast growth factor (bFGF), 0.1 mM 2-mercaptoethanol, L-glutamine, non-essential amino acids and penicillin/streptomycin. hESCs were differentiated to definitive endoderm by culturing for 5 days in RPMI media supplemented with 100 ng/ml of recombinant human activin A, fetal bovine serum (FBS), and penicillin/streptomycin. The concentration of FBS was varied each day as follows: 0.1% (first day), 0.2% (second day), 2% (days 3-5).

Cells were isolated by fluorescence activated cell sorting (FACS) in order to obtain purified populations of hESCs and definitive endoderm for gene expression analysis. Immuno-purification was achieved for hESCs using SSEA4 antigen (R&D Systems, cat# FAB1435P) and for definitive endoderm using CXCR4 (R&D Systems, cat# FAB170P). Cells were dissociated using trypsin/EDTA (Invitrogen, cat# 25300-054), washed in phosphate buffered saline (PBS) containing 2% human serum and resuspended in 100% human serum on ice for 10 minutes to block non-specific binding. Staining was carried out for 30 minutes on ice by adding 200 _(j)ai of phycoerythrin-conjugated antibody to 5×10⁶ cells in 800 _(j)ai human serum. Cells were washed twice with 8 ml of PBS buffer and resuspended in 1 ml of the same. FACS isolation was carried out by the core facility of The Scripps Research Institute using a FACS Vantage (BD Biosciences). Cells were collected directly into RLT lysis buffer and RNA was isolated by RNeasy according to the manufacturers instructions (Qiagen).

Purified RNA was submitted in duplicate to Expression Analysis (Durham, NC) for generation of the expression profile data using the Affymetrix platform and U133 Plus 2.0 high-density oligonucleotide arrays. Data presented is a group comparison that identifies genes differentially expressed between the two populations, hESCs and definitive endoderm. Genes that exhibited a robust upward change in expression level over that found in hESCs were selected as new candidate markers that are highly characteristic of definitive endoderm. Select genes were assayed by Q-PCR, as described above, to verify the gene expression changes found on the gene chip and also to investigate the expression pattern of these genes during a time course of hESC differentiation.

FIGS. 34A-M show the gene expression results for certain markers. Results are displayed for cell cultures analyzed 1, 3 and 5 days after the addition of 100 ng/ml activin A, CXCR4-expressing definitive endoderm cells purified at the end of the five day differentiation procedure (CXDE), and in purified hESCs. A comparison of FIGS. 34C and G-M demonstrates that the six marker genes, FGF17, VWF, CALCR, FOXQ1, CMKORI and CRIP1, exhibit an expression pattern that is almost identical to each other and which is also identical to the pattern of expression of CXCR4 and the ratio of SOX17/SOX7. As described previously, SOX17 is expressed in both the definitive endoderm as well as in the SOX7-expressing extra-embryonic endoderm. Since SOX7 is not expressed in the definitive endoderm, the ratio of SOX17/SOX7 provides a reliable estimate of definitive endoderm contribution to the SOX17 expression witnessed in the population as a whole. The similarity of panels G-L and M to panel C indicates that FGF17, VWF, CALCR, FOXQ1, CMKORI and CRIP1 are likely markers of definitive endoderm and that they are not significantly expressed in extra-embryonic endoderm cells.

It will be appreciated that the Q-PCR results described herein can be further confirmed by ICC.

Example 12 Retinoic Acid and FGF-10 Induces PDX1 Specifically in Definitive Endoderm Cultures

The following experiment demonstrates that RA and FGF-10 induces the expression of PDX1 in definitive endoderm cells.

Human embryonic stem cells were cultured with or without activins for four days. On day four, 1 μM RA and 50 ng/ml FGF-10 were added to the cell culture. Forty-eight hours after the RA/FGF-10 addition, the expression of the PDX1 marker gene and other marker genes not specific to foregut endoderm were quantitated by Q-PCR.

The application of RA to definitive endoderm cells caused a robust increase in PDX1 gene expression (see FIG. 35 ) without increasing the expression of visceral endoderm (50×7, AFP), neural (S OX1, ZIC1), or neuronal (NFM) gene expression markers (see FIG. 36A-F). PDX1 gene expression was induced to levels approximately 500-fold higher than observed in definitive endoderm after 48 hours exposure to 1 μM RA and 50 ng/ml FGF-10. Furthermore, these results show that substantial PDX1 induction occurred only in cell cultures which had been previously differentiated to definitive endoderm (50×17) as indicated by the 160-fold higher PDX1 expression found in the activin treated cell cultures relative to those cultures that received no activin prior to RA application.

Example 13 FGF-10 Provides Additional Increase in PDX1 Expression Over RA Alone

This Example shows that the combination of RA and FGF-10 induces PDX1 expression to a greater extent than RA alone.

As in the previous Example, hESCs were cultured with or without activins for four days. On day four, the cells were treated with one of the following: 1 μM RA alone; 1 μM RA in combination with either FGF-4 or FGF-10; or 1 μM RA in combination with both FGF-4 and FGF-10. The expression of PDX1, SOX7 and NFM were quantitated by Q-PCR ninety six hours after RA or RA/FGF.

The treatment of hESC cultures with activin followed by retinoic acid induced a 60-fold increase in PDX1 gene expression. The addition of FGF-4 to the RA treatment induced slightly more PDX1 (approximately 3-fold over RA alone). However, by adding FGF-10 and retinoic acid together, the induction of PDX1 was further enhanced 60-fold over RA alone (see FIG. 37A). This very robust PDX1 induction was greater than 1400-fold higher than with no activin or RA/FGF treatment. Interestingly, addition of FGF-4 and FGF-10 simultaneously abolished the beneficial effect of the FGF-10, producing only the modest PDX1 increase attributed to FGF-4 addition.

Addition of RA/FGF-4 or RA/FGF-10 combinations did not increase the expression of marker genes not associated with foregut endoderm when compared to cells not exposed to RA/FGF combinations (see FIG. 37B-C).

Example 14 Retinoic Acid Dose Affects Anterior-Posterior (A-P) Position In Vitro

To determine whether the dose of RA affects A-P position in in vitro cell cultures, the following experiment was performed.

Human embryonic stem cells were cultured with or without activins for four days. On day four, FGF-10 at 50 ng/ml was added to the culture in combination with RA at 0.04 μM, 0.2 μM or 1.0 μM. The expression of the PDX1 marker gene as well as other markers not specific for foregut endoderm were quantitated by Q-PCR.

The addition of retinoic acid at various doses, in combination with FGF-10 at 50 ng/ml, induced differential gene expression patterns that correlate with specific anterior-posterior positional patterns. The highest dose of RA (1 μM) preferentially induced expression of anterior endoderm marker (HOXA3) and also produced the most robust increase in PDX1 (FIG. 38A-B). The middle dose of RA (0.2 μM) induced midgut endoderm markers (CDX1, HOXC6) (see FIG. 38C and 41E), while the lowest dose of RA (0.04 μM) preferentially induced a marker of hindgut endoderm (HOXA13) (see FIG. 38D). The RA dose had essentially no effect on the relative expression of either neural (SOX1) or neuronal (NFM) markers (see FIG. 38F-G). This example highlights the use of RA as a morphogen in vitro and in particular as a morphogen of endoderm derivatives of differentiating hESCs.

Example 15 Use of B27 Supplement Enhances Expression of PDX1

PDX1 expression in definitive endoderm can be influenced by the use of a number of factors and cell growth/differentiation conditions. In the following experiment, we show that the use of B27 supplement enhances the expression of PDX1 in definitive endoderm cells.

Human embryonic stem cells were induced to differentiate to definitive endoderm by treatment of undifferentiated hES cells grown on mouse embryonic fibroblast feeders with high dose activin A (100-200 ng/ml in 0.5-2% FBS/DMEM/F12) for 4 days. The no activin A control received 0.5-2% FBS/DMEM/F12 with no added activin A. At four days, cultures received either no activin A in 2% FBS (none), and in 2% serum replacement (SR), or 50 ng/ml activin A together with 2 μM RA and 50 ng/ml FGF-10 in 2% PBS/DMEM/F12 (none, +FBS, +B27) and similarly in 2% Serum replacement (SR). B27 supplement, (Gibco/BRL), was added as a 1/50 dilution directly into 2%FBS/DMEM/F12 (+B27). Duplicate cell samples where taken for each point, and total RNA was isolated and subjected to Q-PCR as previously described.

FIG. 39A-E shows that serum-free supplement B27 provided an additional benefit for induction of PDX1 gene expression without inducing an increase in the expression of markers genes not specific for foregut endoderm as compared to such marker gene expression in cells grown without serum.

Example 16 Use of Activin B to Enhance Induction of PDX1

This Example shows that the use of activin B enhances the differentiation of PDX1-negative cells to PDX1-positive cells in in vitro cell culture.

Human embryonic stem cells were induced to differentiate to definitive endoderm by treatment of undifferentiated hESCs grown on mouse embryonic fibroblast feeders with high dose activin A (50 ng/ml) in low serum/RPMI for 6 days. The FBS dose was 0% on day one, 0.2% on day two and 2% on days 3-6. The negative control for definitive endoderm production (NF) received 2% FBS/RPMI with no added activin A. In order to induce PDX1 expression, each of the cultures received retinoic acid at 2 μM in 2% FBS/RPMI on day 6. The cultures treated with activin A on days one through five were provided with different dosing combinations of activin A and activin B or remained in activin A alone at 50 ng/ml. The no activin A control culture (NF) was provided neither activin A nor activin B. This RA/activin treatment was carried out for 3 days at which time PDX1 gene expression was measured by Q-PCR from duplicate cell samples.

FIG. 40A shows that the addition of activin B at doses ranging from 10-50 ng/ml (a10, a25 and a50) in the presence of 25 ng/ml (A25) or 50 ng/ml (A50) of activin A increased the PDX1 expression at least 2-fold over the culture that received only activin A at 50 ng/ml. The increase in PDX1 as a result of activin B addition was without increase in HNF6 expression (see FIG. 40B), which is a marker for liver as well as pancreas at this time in development. This result suggests that the proportion of cells differentiating to pancreas had been increased relative to liver.

Example 17 Use of Serum Dose to Enhance Induction of PDX1

The expression of PDX1 in definitive endoderm cells is influenced by the amount of serum present in the cell culture throughout the differentiation process. The following experiment shows that the level of serum in a culture during the differentiation of hESCs to PDX1-negative definitive endoderm has an effect on the expression of PDX1 during further differentiation of these cells to PDX1-positive endoderm.

Human embryonic stem cells were induced to differentiate to definitive endoderm by treatment of undifferentiated hESCs grown on mouse embryonic fibroblast feeders with high dose activin A (100 ng/ml) in low serum/RPMI for 5 days. The FBS dose was 0.1% on day one, 0.5% on day two and either 0.5%, 2% or 10% on days 3-5. The no activin A control (NF) received the same daily FBS/RPMI dosing, but with no added activin A. PDX1 expression was induced beginning at day 6 by the addition of RA. During days 6-7, cultures received retinoic acid at 2 μM in 0.5% FBS/RPMI, 1 μM on day 8 and 0.2 μM on day 9-11. The activin A was lowered to 50 ng/ml during retinoic acid treatment and was left absent from the no activin A control (NF).

FIG. 41A shows that the FBS dosing during the 3 day period of definitive endoderm induction (days 3, 4 and 5) had a lasting ability to change the induction of PDX1 gene expression during the retinoic acid treatment. This was without significant alteration in the expression pattern of ZIC1 (FIG. 41B) or SOX7 (FIG. 41C) gene expression.

Example 18 Use of Conditioned Medium to Enhance Induction of PDX1

Other factors and growth conditions which influence the expression of PDX1 in definitive endoderm cells were also studied. The following experiment shows the effect of conditioned media on the differentiation of PDX1-negative definitive endoderm cells to PDX1-positive e ndoderm cells.

Human embryonic stem cells were induced to differentiate to definitive endoderm by treatment of undifferentiated hESCs grown on mouse embryonic fibroblast feeders with high dose activin A (100 ng/ml) in low serum/RPMI for 5 days. The FBS dose was 0.2% on day one, 0.5% on day two and 2% on days 3-5.

The definitive endoderm cultures generated by 5 days of activin A treatment were then induced to differentiate to PDX1 expressing endoderm by the addition of RA in 2% FBS/RPMI containing activin A at 25 ng/ml for four days. The RA was 2 _(l)a M for the first two days of addition, 1 μM on the third day and 0.5 μM on the fourth day. This base medium for PDX1 induction was provided fresh (2A25R) or after conditioning for 24 hours by one of four different cell populations. Conditioned media (CM) were generated from either mouse embryonic fibroblasts (MEFCM) or from hESCs that were first differentiated for 5 days by one of three conditions; i) 3% FBS/RPMI (CM2), or ii) activin A (CM3) or iii) bone morphogenic protein 4 (BMP4) (CM4). Activin A or BMP4 factors were provided at 100 ng/ml under the same FBS dosing regimen described above (0.2%, 0.5%, 2%). These three different differentiation paradigms yield three very different populations of human cells by which the PDX1 induction media can be conditioned. The 3% FBS without added growth factor (NF) yields a heterogeneous population composed in large part of extraembryonic endoderm, ectoderm and mesoderm cells. The activin A treated culture (A100) yields a large proportion of definitive endoderm and the BMP4 treated culture (B100) yields primarily trophectoderm and some extraembryonic endoderm.

FIG. 42A shows that PDX1 was induced equivalently in fresh and conditioned media over the first two days of RA treatment. However, by the third day PDX1 expression had started to decrease in fresh media and MEF conditioned media treatments. The differentiated hESCs produced conditioned media that resulted in maintenance or further increases in the PDX1 gene expression at levels 3 to 4-fold greater than fresh media. The effect of maintaining high PDX1 expression in hESC-conditioned media was further amplified on day four of RA treatment achieving levels 6 to 7-fold higher than in fresh media. FIG. 42B shows that the conditioned media treatments resulted in much lower levels of CDX1 gene expression, a gene not expressed in the region of PDX1 expressing endoderm. This indicates that the overall purity of PDX1-expressing endoderm was much enhanced by treating definitive endoderm with conditioned media generated from differentiated hESC cultures.

FIG. 43 shows that PDX1 gene expression exhibited a positive dose response to the amount of conditioned media applied to the definitive endoderm cells. Total volume of media added to each plate was 5 ml and the indicated volume (see FIG. 43 ) of conditioned media was diluted into fresh media (A25R). It is of note that just 1 ml of conditioned media added into 4 ml of fresh media was still able to induce and maintain higher PDX1 expression levels than 5 ml of fresh media alone. This suggests that the beneficial effect of conditioned media for induction of PDX1 expressing endoderm is dependent on the release of some substance or substances from the cells into the conditioned media and that this substance(s) dose dependently enhances production of PDX1-expressing endoderm.

Example 19 Validation of Antibodies Which Bind to PDX1

Antibodies that bind to PDX1 are useful tools for monitoring the induction of PDX1 expression in a cell population. This Example shows that rabbit polyclonal and IgY antibodies to PDX1 can be used to detect the presence of this protein.

In a first experiment, IgY anti-PDX1 (IgY α-PDX1) antibody binding to PDX1 in cell lysates was validated by Western blot analysis. In this analysis, the binding of IgY oc-PDX1 antibody to 50 _(l)ag of total cell lysate from MDX12 human fibroblasts or MDX12 cells transfected 24 hrs previously with a PDX1 expression vector was compared. The cell lysates separated by SDS-PAGE, transferred to a membrane by electroblotting, and then probed with the IgY oc-PDX1 primary antiserum followed by alkaline phosphatase conjugated rabbit anti-IgY (Rb ct-IgY) secondary antibodies. Different dilutions of primary and secondary antibodies were applied to separate strips of the membrane in the following combinations: A (500x dilution of primary, 10,000× dilution of secondary), B (2,000×, 10,000×), C (500×, 40,000×), D (2,000×, 40,000), E (8,000×, 40,000×).

Binding was detected in cells transfected with the PDX1 expression vector (PDX1-positive) at all of the tested antibody combinations. Binding was only observed in untransfected (PDX1-negative) fibroblasts when using the highest concentrations of both primary and secondary antibody together (combination A). Such non-specific binding was characterized by the detection of an additional band at a molecular weight slightly higher than PDX1 in both the transfected and untransfected fibroblasts.

In a second experiment, the binding of polyclonal rabbit anti-PDX1 (Rb PDX1) antibody to PDX1 was tested by immunocytochemistry. To produce a PDX1 expressing cell for such experiments, MS1-V cells (ATCC # CRL-2460) were transiently transfected with an expression vector of PDX1-EGFP (constructed using pEGFP-N1, Clontech). Transfected cells were then labeled with Rb oc-PDX1 and oc-EGFP antisera. Transfected cells were visualized by both EGFP fluorescence as well as oc-EGFP immunocytochemistry through the use of a Cy5 conjugated secondary antibody. PDX1 immunofluorescence was visualized through the use of an oc-Rb Cy3-conjugated secondary antibody.

Binding of the Rb oc-PDX1 and the oc-EGPF antibodies co-localized with GPF expression.

Example 20 Immunocytochemistry of Human Pancreatic Tissue

This Example shows that antibodies having specificity for PDX1 can be used to identify human PDX1-positive cells by immunocytochemistry.

In a first experiment, paraffin embedded sections of human pancreas were stained for insulin with guinea pig anti-insulin (Gp α-Ins) primary antibody at a 1/200 dilution followed by dog anti-guinea pig (D α-Gp) secondary antibody conjugated to Cy2 at a 1/100 dilution. In a second experiment, the same paraffin embedded sections of human pancreas were stained for PDX1 with IgY α-PDX1 primary antibody at a 1/4000 dilution followed Rb α-IgY secondary antibody conjugated to AF555 at a 1/300 dilution. The images collected from the first and second experiments where then merged. In a third experiment, cells that were stained with IgY α-PDX1 antibodies were also stained with DAPI.

Analysis of the human pancreatic sections revealed the presence of strong staining of islets of Langerhans. Although the strongest PDX1 signal appeared in islets (insulin-positive), weak staining was also seen in acinar tissue (insulin-negative). DAPI and PDX1 co-staining shows that PDX1 was mostly but not exclusively localized to the nucleus.

Example 21 Immunoprecipitation of PDX1 from Retinoic Acid Treated Cells

To further confirm PDX1 expression in definitive endoderm cells that have been differentiated in the presence of RA and the lack of PDX1 in definitive endoderm cells that have not been differentiated with RA, a rabbit anti-PDX1 (Rb α-PDX1) antibody was used to immunoprecipitate PDX1 from both RA differentiated and undifferentiated definitive endoderm cells Immunoprecipitated RA was detected by Western blot analysis using IgY α-PDX1 antibody.

To obtain undifferentiated and differentiated definitive endoderm cell lysates for immunoprecipitation, hESCs were treated for 5 days with activin A at 100 ng/ml in low serum (definitive endoderm) followed by treatment with activin A at 50 ng/ml and 2 μM all-trans RA for two days, 1 μM for one day and 0.2 pM for one day (PDX1-positive foregut endoderm). As a positive control cell lysates were also prepared from MS1-V cells (ATCC # CRL-2460) transfected with a PDX1 expression vector. PDX1 was immunoprecipitated by adding Rb α-PDX1 and rabbit-specific secondary antibodies to each lysate. The precipitate was harvested by centrifugation Immunoprecipitates were dissolved in SDS-containing buffer then loaded onto a polyacrylamide gel. After separation, the proteins were transferred to a membrane by electroblotting, and then probed with the IgY α-PDX1 primary antibody followed by labeled Rb α-IgY secondary antibodies.

Immunoprecipitates collected from the MS1-V positive control cells as well as those from day 8 (lane d8, three days after the start of RA treatment) and day 9 (lane d9, four days after the start of RA) cells were positive for PDX1 protein (FIG. 44 ). Precipitates obtained from undifferentiated definitive endoderm cells (that is, day 5 cells treated with activin A — designated (A) in FIG. 44 ) and undifferentiated hESCs (that is, untreated day 5 cells — designated as (NF) in FIG. 44 ) were negative for PDX1.

Example 22

Generation of PDX1 Promoter-EGFP Transgenic hESC Lines

In order to use the PDX1 marker for cell isolation, we genetically tagged PDX1-positive foregut endoderm cells with an expressible reporter gene. This Example describes the construction of a vector comprising a reporter cassette which comprises a reporter gene under the control of the PDX1 regulatory region. This Example also describes the preparation of a cell, such as a human embryonic stem cell, transfected with this vector as well as a cell having this reporter cassette integrated into its genome.

PDX1-expressing definitive endoderm cell lines genetically tagged with a reporter gene were constructed by placing a GFP reporter gene under the control of the regulatory region (promoter) of the PDX1 gene. First, a plasmid construct in which EGFP expression is driven by the human PDX1 gene promoter was generated by replacing the CMV promoter of vector pEGFP-N1 (Clontech) with the human PDX1 control region (Genbank Accession No. AF192496, the disclosure of which is incorporated herein by reference in its entirety), which comprises a nucleotide sequence ranging from about 4.4 kilobase pairs (kb) upstream to about 85 base pairs (bp) downstream of the PDX1 transcription start site. This region contains the characterized regulatory elements of the PDX1 gene, and it is sufficient to confer the normal PDX1 expression pattern in transgenic mice. In the resulting vector, expression of EFGP is driven by the PDX1 promoter. In some experiments, this vector can be transfected into hESCs.

The PDX1 promoter/EGFP cassette was excised from the above vector, and then subcloned into a selection vector containing the neomycin phosphotransferase gene under control of the phosphoglycerate kinase-1 promoter. The selection cassette was flanked by flp recombinase recognition sites to allow removal of the cassette. This selection vector was linearized, and then introduced into hESCs using standard lipofection methods. Following 10-14 days of selection in G418, undifferentiated transgenic hESC clones were isolated and expanded.

Example 23 Isolation of PDX1-Positive Foregut Endoderm

The following Example demonstrates that hESCs comprising the PDX1 promoter/EGFP cassette can be differentiated into PDX1-positive endoderm cells and then subsequently isolated by fluorescence-activated cell sorting (FACS).

PDX1 promoter/EGFP transgenic hESCs were differentiated for 5 days in activin A-containing media followed by two days in media comprising activin A and RA. The differentiated cells were then harvested by trypsin digestion and sorted on a Becton Dickinson FACS Diva directly into RNA lysis buffer or PBS. A sample of single live cells was taken without gating for EGFP (Live) and single live cells were gated into EGFP positive (GFP) and GFP negative (Neg) populations. In one experiment, the EGFP positive fraction was separated into two equally sized populations according to fluorescence intensity (Hi and Lo).

Following sorting, cell populations were analyzed by both Q-PCR and immunocytochemistry. For Q-PCR analysis, RNA was prepared using Qiagen RNeasy columns and then converted to cDNA. Q-PCR was conducted as described previously. For immunocytochemistry analysis, cells were sorted into PBS, fixed for 10 minutes in 4% paraformaldehyde, and adhered to glass slides using a Cytospin centrifuge. Primary antibodies to Cytokeratin19 (KRT19) were from Chemicon; to Hepatocyte nuclear factor 3 beta (HNF313) from Santa Cruz; to Glucose Transporter 2 (GLUT2) from R&D systems. Appropriate secondary antibodies conjugated to FITC (green) or Rhodamine (Red) were used to detect binding of the primary antibodies.

A typical FACS sort of differentiated cells is shown in FIG. 45 . The percent isolated PDX1-positive cells in this example was approximately 7%, which varied depending on the differentiation efficiency from about 1% to about 20%.

Sorted cells were further subjected to Q-PCR analysis. Differentiated cells showed a correlation of EGFP fluorescence with endogenous PDX1 gene expression. Compared to non-fluorescing cells, the EGFP positive cells showed a greater than 20-fold increase in PDX1 expression levels (FIG. 46 ). The separation of high and low EGFP intensity cells indicated that EGFP expression level correlated with PDX1 expression level (FIG. 47 ). In addition to PDX1 marker analysis, sorted cells were subjected to Q-PCR analysis of several genes that are expressed in pancreatic endoderm. Products of each of these marker genes (NKX2.2, GLUT2, KRT19, HNF4c and HNF3(3) were all enriched in the EGFP positive fraction (FIGS. 48A-E). In contrast, the neural markers ZIC1 and GFAP were not enriched in sorted EGFP expressing cells (FIGS. 49A and B).

By immunocytochemistry, virtually all the isolated PDX1-positive cells were seen to express KRT19 and GLUT2. This result is expected for cells of the pancreatic endoderm lineage. Many of these cells were also HNF313 positive by antibody staining

Example 24

Production of PDX1-positive Dorsal and Ventral Foregut Endoderm

This Example describes the production of PDX1-positive, dorsally-biased, foregut endoderm as well as the production of PDX1-positive, ventrally-biased, foregut endoderm.

Definitive endoderm was produced from undifferentiated hESCs using a three or five day protocol in which activin A was provided to the culture medium at a concentration of 100 ng/ml each day. For both dorsal and ventral differentiation, the medium composition for the first five days was as follows: Day1−RPMI+0% fetal bovine serum (FBS), Day 2−RPMI+0.2% PBS, Day 3−RPMI+2.0% FBS, Day 4−RPMI+2.0% FBS and Day 5−RPMI +2.0% PBS. For the ventral differentiation, definitive endoderm was produced for 3 days in activin A at 100 ng/ml and then exposed to BMP4 at 3 ng/ml and FGF10 at 50 ng/ml. BMP4/FGF10 addition was carried out in RPMI +2% FBS for the first 2 days and then subsequently in Connaught Medical Research Labs (CMRL) medium (Invitrogen, Carlsbad, Calif.) (see, Parker R. C., et al. 1957. N.Y. Academy of Sciences 5:303, the disclosure of which is incorporated herein by reference in its entirety) containing B27 supplement (1 part B27 to 200 parts medium by volume — (1:200)) (Invitrogen, Carlsbad, Calif.). For the dorsal differentiation procedure, definitive endoderm was produced for 5 days in activin A at 100 ng/ml and then exposed to retinoic acid (RA) at 2 μM and activin A at 25 ng/ml in CMRL medium containing B27 supplement (1:200).

In the RA-based, dorsal differentiation procedure, there was a strong induction of PDX1 and a maintenance of HB9 expression with no induced expression of HHEX or albumin, which are ventral liver markers (FIGS. 50A-D). In the ventral differentiation protocol, which does not use RA but instead uses FGF10 and BMP, PDX1 gene expression was also strongly induced. In contrast to the RA treatment, HB9 (dorsal endoderm marker) expression was not maintained and ventral liver markers, such as albumin and HHEX, were strongly induced along with PDX1 (FIGS. 50A-D). These data indicated that in the presence of RA, the foregut PDX1-expressing endoderm was devoid of liver (a ventral organ) markers and expressed dorsal markers like HB9. In the absence of RA, the PDX1 expression was not accompanied by high HB9 expression levels. Furthermore, the expression of classical liver markers, such as albumin and HHEX, indicated that the definitive endoderm was preferentially executing a ventral differentiation program since liver is exclusively derived from the ventral endoderm.

Example 25

Production of PDX1-positive Ventral Foregut Endoderm Cells is Dependent on Definitive Endoderm Formation

This Example describes the production of PDX1-positive, ventrally-biased, foregut endoderm from cultures comprising varying amounts of definitive endoderm cells. Cultures with no definitive endoderm show very little production of PDX1-positive, ventrally biased, foregut endoderm. As the initial amount of definitive endoderm cells increase, so does the production of ventrally-biased, foregut endoderm.

Four separate conditions were used to treat hESCs that result in varying proportions of differentiation to definitive endoderm. All four conditions utilized RPMI supplemented with 0% FBS on the first day, 0.2% FBS on second day, and 2% FBS on days 3 and 4. The four conditions were as follows: (a) BMP4 at 100 ng/mL with SU5402 at 5 _(l)a M; (b) no exogenous growth factors; (c) activin A at 15 ng/mL; and (d) activin A at 100 ng/ml. After the first four days of differentiation, the relative levels of definitive endoderm produced were indicated by cerberus (CER) and SOX17 expression levels, whereby definitive endoderm was essentially absent under condition (a), minimal under condition (b), present under condition (c) and highly present under condition (d). All cultures were then incubated for 2 days with BMP4 at 3 ng/mL, FGF10 at 50 ng/ml and KAAD-cyclopamine at 0.5 μM in a base medium of 2% FBS in RPMI followed by 6 days with BMP4 at 3 ng/mL, FGF10 at 50 ng/ml and KAAD-cyclopamine at 0.5 μM in a base medium composed of CMRL with 1:200 dilution of B27 extract.

In the presence of SU5402 and BMP4, conditions under which no definitive endoderm was produced as demonstrated by lack of CER and SOX17 gene expression (FIGS. 51A and 51B), there was no induction of PDX1 or albumin gene expression after treatment with BMP4/FGF10 (ventral endoderm condition) (FIGS. 51C and 51D). This was similarly true for the no growth factor condition (condition (b)), in which very minimal levels of definitive endoderm were formed as indicated by the low levels of CER and SOX17 (FIGS. 51A and 51B). Although PDX1 and albumin gene expression was very low under the no growth factor condition (FIGS. 51C and 51D), the amount of gene expression was significantly greater than that produced from condition (a). The hESCs treated with intermediate (15 ng/ml) and high (100 ng/ml) doses of activin A yielded robust definitive endoderm differentiation, indicated by high SOX17 gene expression levels (FIG. 51B). The high dose activin treatment produced definitive endoderm primarily of anterior character as indicated by very high CER expression levels. Both the condition (c) and condition (d) treatments exhibited robust ventral endoderm differentiation as indicated by high level PDX1 and albumin gene expression (FIGS. 51C and 51D). The levels of PDX1 and albumin expression were greatest in the most anterior endoderm because anterior endoderm remains competent to differentiate to more posterior endoderm fates while posterior endoderm cells have lost competence to acquire more anterior fates. These data strongly indicated that the production of ventral PDX1-expressing foregut endoderm and liver were dependent upon efficient production of definitive endoderm.

Example 26

BMP4 is not Necessary for PDX1-positive Ventral Foregut Endoderm

This Example describes the production of PDX1-positive, ventrally-biased, foregut endoderm in the absence of BMP4.

Definitive endoderm was produced by exposing undifferentiated hESCs to activin at 100 ng/mL in RPMI base medium supplemented with 0%, 0.2%, and 2% FBS on days 1 through 3, respectively. After 3 days of activin A treatment, the cultures were switched to a base medium composed of RPMI containing 2% FBS and maintained under one of the following conditions: (a) BMP4 at 3 ng/ml with FGF10 at 50 ng/ml and KAAD-cyclopamine at 0.5 μM; (b) FGF10 at 50 ng/ml and KAAD-cyclopamine at 0.5 μM; or (c-e) no exogenous factors. After two days, the base medium was changed to CMRL plus B27 supplement (1:200) and cells were maintained according to conditions (a-c) above. Alternatively, cells were maintained with no exogenous factors in RPMI with B27 supplement (1:200) (condition (d)) or RPMI with 2% FBS (condition (e)). The same factor treatment conditions were maintained for 8 more days of differentiation.

BMP4 was not needed to produce either PDX1-positive ventral foregut or liver endoderm cells as indicated by the robust induction of PDX1 and albumin expression in the absence of BMP4 (FIGS. 52A and 52B). BMP4 addition appeared to be less favorable for the production of PDX1-positive ventral foregut endoderm but the addition of BMP4 to FGF10 and KAAD-cyclopamine treatment does not decrease ventral foregut liver endoderm gene expression (FIGS. 52A and 52B). The use of CMRL with B27 supplement had some ability to induce PDX1 expression in the absence of added factors (condition (c)) while RPMI with B27 (condition (d)) and RPMI with 2% FBS (condition (e)) did not exhibit any induction of PDX1 expression (FIG. 52A). There did not appear to be a significant effect of base media on the induction of liver gene expression. In summary, FGF10 and KAAD-cyclopamine are sufficient to produce PDX1-positive ventral foregut endoderm.

Example 27 Markers for the Identification of PDX1-positive Dorsal and Ventral Foregut Endoderm

This Example describes markers useful for, among other things, the identification, detection, enrichment, isolation, purification, targeting and/or validation of PDX1-positive dorsal and ventral foregut endoderm.

Cell cultures differentiated as described in Example 24 were subjected to gene chip analysis to globally monitor the gene expression dynamics occurring during differentiation of hESC to definitive endoderm and further on to more mature dorsal and ventral endoderm phenotypes. Duplicate samples were isolated at the times indicated in Example 24. Gene expression profiles were determined using Affymetrix U133 plus 2.0 high density oligonucleotide arrays by Expression Analysis (Durham, NC) according to their internal standard operating procedures. We have evaluated the patterns of gene expression across these 7 conditions/time points through manual inspection as well as through hierarchical clustering analyses. We have looked for patterns of gene expression that match the temporal pattern of PDX1 expression (dorsal and ventral) to find novel genes that are expressed in both ventral and dorsal differentiation paradigms.

Provided are genes that have a significant similarity in expression pattern to PDX1, and thus, may be co-expressed in PDX1-expressing foregut endoderm cells The genes listed in Table 3 are expressed in both the dorsal and ventral PDX1 differentiation. The genes in Table 4 are dorsally biased and are preferentially expressed in the dorsal PDX1 pattern.

Table 3 lists 39 markers that are expressed in both dorsal and ventral PDX1-positive foregut endoderm. Column 1 provides the commonly known gene symbol for each marker. Columns 2 through 4 provide the Unigene, LocusLink, and OMIM accession numbers, respectively. Column 5 described the Genebank accession number for a nucleic acid sequence which includes the marker described in column 1 Finally, column 6 provides a description of the functional activity of the polypeptide marker that is encoded by the listed genetic marker.

It will be appreciated that the accession numbers listed in Table 3 can be used by those of ordinary skill in the art to retrieve specific information about each sequence described in the table, including both the primary nucleic acid and polypeptide sequence of each of these marker.

TABLE 3 Markers expressed in both dorsal and ventral PDX1-positive foregut endoderm Gene_Symbol Unigene LocusLink OMIM SeqDerivedFrom Gene Descriptor ANXA4 Hs.422986 307 106491 NM_001153 annexin A4 ASCL1 Hs.524672 429 100790 BC001638 achaete-scute complex-like 1 (Drosophila) BNC1 Hs.459153 646 601930 NM_001717 basonuclin 1 C10orf30 Hs.498740 222389 AW195407 Chromosome 10 open reading frame 30 C2orf23 Hs.368884 65055 609139 BE535746 chromosome 2 open reading frame 23 C9orf150 Hs.445356 286343 AI972386 chromosome 9 open reading frame 150 CDH6 Hs.171054 1004 603007 BC000019 cadherin 6, type 2, K-cadherin (fetal kidney) DACH1 Hs.129452 1602 603803 AI650353 dachshund homolog 1 (Drosophila) DUSP9 Hs.144879 1852 300134 NM_001395 dual specificity phosphatase 9 ELMOD1 Hs.495779 55531 AL359601 ELMO domain containing 1 FLJ21462 fis Hs.24321 AW236803 CDNA clone IMAGE: 5273964, partial cds FLJ22761 Hs.522988 80201 W81116 hypothetical protein FLJ22761 GABRA2 Hs.116250 2555 137140 NM_000807 gamma-aminobutyric acid (GABA) A receptor, alpha 2 GRIA3 Hs.377070 2892 305915 BC032004 glutamate receptor, ionotrophic, AMPA 3 HNF4G Hs.241529 3174 605966 AI916600 hepatocyte nuclear factor 4, gamma IDH2 Hs.513141 3418 147650 U52144 isocitrate dehydrogenase 2 (NADP+), mitochondrial IL6R Hs.135087 3570 147880 AV700030 interleukin 6 receptor KCNJ2 Hs.1547 3759 170390 AF153820 potassium inwardly-rectifying channel, subfamily J, member 2 KLF3 Hs.298658 51274 AA130132 Kruppel-like factor 3 (basic) LGALS3 Hs.531081 3958 153619 AW085690 Lectin, galactoside-binding, soluble, 3 (galectin 3) LGALS3 /// GALIG Hs.531081 3958/// 153619 BC001120 lectin, galactoside-binding, soluble, 3 (galectin 3) /// galectin-3 internal gene LIPC Hs.188630 3990 151670 NM_000236 lipase, hepatic MEIS1 Hs.526754 4211 601739 NM_002398 Meis1, myeloid ecotropic viral integration site 1 homolog (mouse) NR2F1 Hs.519445 7025 132890 AI951185 Nuclear receptor subfamily 2, group F, member 1 ONECUT2 Hs.194725 9480 604894 NM_004852 one cut domain, family member 2 PAPPA Hs.494928 5069 176385 AA148534 pregnancy-associated plasma protein A, pappalysin 1 PDE3B Hs.445711 5140 602047 NM_000753 phosphodiesterase 3B, cGMP-inhibited PGPEP1 Hs.131776 54858 NM_017712 pyroglutamyl-peptidase I PMS2L1 Hs.520575 5379 605038 D38503 postmeiotic segregation increased 2-like 1 SERPINF2 Hs.159509 5345 262850 NM_000934 serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2 SLC27A2 Hs.11729 11001 603247 NM_003645 solute carrier family 27 (fatty acid transporter), member 2 SLN Hs.334629 6588 602203 NM_003063 sarcolipin SOX9 Hs.2316 6662 114290 NM_000346 SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal) SULT2A1 Hs.515835 6822 125263 U08024 sulfotransferase family, cytosolic, 2A, dehydroepiandrosterone (DHEA)-preferring, member 1 TFPI Hs.516578 7035 152310 BF511231 Tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) ZHX1 Hs.521264 11244 604764 AI123518 zinc fingers and homeoboxes 1 ZNF467 Hs.112158 168544 BE549732 zinc finger protein 467 ZNF503 Hs.195710 84858 AA603467 zinc finger protein 503 Hs.142869 AI935586 Transcribed locus

FIGS. 53A-E further illustrate the commonality of expression profile between PDX1 and markers selected from Table 3. In particular, FIGS. 53A-E provide examples of genes that displayed nearly identical gene expression patterns to that of PDX1 across the 7 conditions/time monitored in this experiment. Pattern recognition to this degree of similarity most likely reflects co-expression of these genes in the same cells that express PDX1, thus making these markers excellent novel candidate markers for PDX1-positive foregut endoderm from both dorsal and ventral endoderm origins.

Table 4 lists 50 markers that are specifically and/or preferentially expressed in dorsal PDX1-positive foregut endoderm. Column 1 provides the commonly known gene symbol for each marker. Columns 2 through 4 provide the Unigene, LocusLink, and OMIM accession numbers, respectively. Column 5 described the Genebank accession number for a nucleic acid sequence which includes the marker described in column 1 Finally, column 6 provides a description of the functional activity of the polypeptide marker that is encoded by the listed genetic marker.

It will be appreciated that the accession numbers listed in Table 4 can be used by those of ordinary skill in the art to retrieve specific information about each sequence described in the table, including both the primary nucleic acid and polypeptide sequence of each of these marker.

TABLE 4 Markers expressed in dorsally-biased PDX1-positive foregut endoderm Gene_Symbol Unigene LocusLink OMIM SeqDerivedFrom Gene Descriptor ADORA2A Hs.197029 135 102776 NM_000675 adenosine A2a receptor AMSH-LP Hs.16229 57559 AI638611 associated molecule with the SH3 domain of STAM (AMSH) like protein BAIAP2L1 Hs.489237 55971 AA628400 BAI1-associated protein 2-like 1 CD47 Hs.446414 961 601028 BG230614 CD47 antigen (Rh-related antigen, integrin-associated signal transducer) CHN2 Hs.203663 1124 602857 AK026415 Chimerin (chimaerin) 2 CLDN3 Hs.25640 1365 602910 BE791251 claudin 3 CPVL Hs.233389 54504 NM_031311 carboxypeptidase, vitellogenic-like /// carboxypeptidase, vitellogenic-like CREB3L1 Hs.405961 90993 AF055009 cAMP responsive element binding protein 3-like 1 DACT1 Hs.48950 51339 607861 NM_016651 dapper homolog 1, antagonist of beta-catenin (xenopus) DPP6 Hs.490684 1804 126141 AW071705 Dipeptidylpeptidase 6 ELF3 Hs.67928 1999 602191 AF017307 E74-like factor 3 (ets domain transcription factor, epithelial-specific) ENPP2 Hs.190977 5168 601060 L35594 ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin) EPB41L1 Hs.437422 2036 602879 AA912711 erythrocyte membrane protein band 4.1-like 1 FAM46C Hs.356216 54855 AL046017 family with sequence similarity 46, member C FAM49A Hs.467769 81553 NM_030797 family with sequence similarity 49, member A /// family with sequence similarity 49, member A FLJ30596 Hs.81907 133686 AI453203 hypothetical protein FLJ30596 HOXA1 Hs.67397 3198 142955 S79910 homeo box A1 HOXA3 Hs.533357 3200 142954 AW137982 homeo box A3 HOXB2 Hs.514289 3212 142967 NM_002145 homeo box B2 LAF4 Hs.444414 3899 601464 AW085505 Lymphoid nuclear protein related to AF4 LOC283658 Hs.87194 283658 AA233912 hypothetical protein LOC283658 MAF Hs.134859 4094 177075 AF055376 v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian) MAG Hs.515354 4099 159460 X98405 myelin associated glycoprotein MYCPBP Hs.513817 10260 600382 BE268538 c-myc promoter binding protein NR4A2 Hs.165258 4929 168600/ NM_006186 nuclear receptor subfamily 4, group A, member 2 NRXN3 Hs.368307 9369 600567 AI129949 neurexin 3 NSE1 Hs.260855 151354 AI601101 NSE1 PCGF5 Hs.500512 84333 AL045882 polycomb group ring finger 5 PDE11A Hs.130312 50940 604961 AB038041 phosphodiesterase 11A PDE5A Hs.370661 8654 603310 BF221547 Phosphodiesterase 5A, cGMP-specific PGA3 5220 169710 AI570199 pepsinogen 3, group I (pepsinogen A) PLN Hs.170839 5350 115200 NM_002667 phospholamban PTGIS Hs.302085 5740 145500 NM_000961 prostaglandin I2 (prostacyclin) synthase /// prostaglandin I2 (prostacyclin) synthase RARB Hs.436538 5915 180220 NM_000965 retinoic acid receptor, beta RGN Hs.77854 9104 300212 D31815 regucalcin (senescence marker protein-30) RND1 Hs.124940 27289 609038 U69563 Rho family GTPase 1 SFRP5 Hs.279565 6425 604158 NM_003015 secreted frizzled-related protein 5 SGKL Hs.380877 23678 607591 AV690866 serum/glucocorticoid regulated kinase-like SLC16A10 Hs.520321 117247 607550 N30257 solute carrier family 16 (monocarboxylic acid transporters), member 10 SLC16A2 Hs.75317 6567 300095 NM_006517 solute carrier family 16 (monocarboxylic acid transporters), member 2 SLC1A3 Hs.481918 6507 600111 NM_004172 solute carrier family 1 (glial high affinity glutamate transporter), member 3 SLC30A4 Hs.162989 7782 602095 NM_013309 solute carrier family 30 (zinc transporter), member 4 SLICK Hs.420016 343450 AI732637 sodium- and chloride-activated ATP-sensitive potassium channel SLITRK4 Hs.272284 139065 AL080239 SLIT and NTRK-like family, member 4 ST8SIA3 Hs.298923 51046 NM_015879 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3 WNT5A Hs.152213 7474 164975 AI968085 wingless-type MMTV integration site family, member 5A /// wingless-type MMTV integration site family, member 5A XPR1 Hs.227656 9213 605237 AF089744 xenotropic and polytropic retrovirus receptor Hs.535688 AK001582 CDNA FLJ10720 fis, clone NT2RP3001116 Hs.127009 AI935541 Transcribed locus Hs.4749 AL137310 CDNA FLJ31660 fis, clone NT2RI2004410

FIG. 54A-D provide examples of genes that display patterns of gene expression that indicate specific (HOXA1 and PDE11A) or preferential (FAM49A and WNTSA) expression in the dorsal endoderm condition (RA treatment). These markers are novel candidate genes for identification of PDX1-positive, dorsally-biased, foregut endoderm.

Example 28 Production of PDX1-Negative Foregut Endoderm

This Example describes the production of PDX1-negative foregut endoderm.

Human embryonic stem cells were differentiated for 7 days via a 2-step protocol to achieve PDX1 cells. The first step comprised 5 days differentiation in activin A (100 ng/ml) to robustly produce DE (D′Amour, K., et al., Nature Biotechnology 23, 1534-1541, (2005)). Step 2 comprised 2 days differentiation in fresh RPMI with 2% FBS containing FGF10 (50 ng/ml) and KAAD-cyclopamine (0.5 μM).

The addition of FGF10 (5-500 ng/ml) was beneficial together with the addition of KAAD-cyclopamine (0.1-2 μM, sonic hedgehog inhibitor), which further specified definitive endoderm cells into the foregut endoderm domain.

The methods, compositions, and devices described herein are presently representative of preferred embodiments and are exemplary and are not intended as limitations on the scope of the invention. Changes therein and other uses will occur to those skilled in the art which are encompassed within the spirit of the invention and are defined by the scope of the disclosure. Accordingly, it will be apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention.

As used in the claims below and throughout this disclosure, by the phrase “consisting essentially of” is meant including any elements listed after the phrase, and limited to other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase “consisting essentially of” indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they affect the activity or action of the listed elements.

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What is claimed is:
 1. A method of producing human pancreatic-duodenal homeobox factor-1 (PDXI)-positive ventrally-biased foregut endoderm cells, comprising: culturing human definitive endoderm cells in a medium comprising an effective amount of a fibroblast growth factor (FGF)-family growth factor to promote differentiation of the human definitive endoderm cells to produce PDX I-positive ventrally-biased foregut endoderm cells.
 2. The method of claim 1, wherein the FGF-family growth factor is FGF-7 or FGF-10.
 3. The method of claim 1, wherein the medium comprises the FGF-family growth factor at a concentration of 5 ng/ml to 500 ng/ml.
 4. A method of producing human PDXI-positive dorsally-biased foregut endoderm cells, comprising: culturing human definitive endoderm cells in a medium comprising an effective amount of a retinoid to promote differentiation of the human definitive endoderm cells to produce PDX I-positive dorsally-biased foregut endoderm cells.
 5. The method of claim 4, wherein the retinoid is RA.
 6. The method of claim 5, wherein the medium comprises RA at a concentration of 0.2 μM to 2.0 μM. 